diff --git a/project/graphql/biolink_model.graphql b/project/graphql/biolink_model.graphql index 919bbdc58..cc286c80d 100644 --- a/project/graphql/biolink_model.graphql +++ b/project/graphql/biolink_model.graphql @@ -1,5 +1,3 @@ -# metamodel_version: 1.7.0 -# version: 4.2.2 type AccessibleDnaRegion implements GenomicEntity, ChemicalEntityOrGeneOrGeneProduct, PhysicalEssence, OntologyClass { id: String! diff --git a/project/jsonld/biolink_model.context.jsonld b/project/jsonld/biolink_model.context.jsonld index c09ee866b..172daab05 100644 --- a/project/jsonld/biolink_model.context.jsonld +++ b/project/jsonld/biolink_model.context.jsonld @@ -1,11 +1,10 @@ { "comments": { "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2024-09-23T16:44:56", + "generation_date": "2024-09-23T23:51:05", "source": "biolink_model.yaml" }, "@context": { - "xsd": "http://www.w3.org/2001/XMLSchema#", "AGRKB": "https://www.alliancegenome.org/", "APO": { "@id": "http://purl.obolibrary.org/obo/APO_", @@ -579,6 +578,7 @@ "@id": "http://www.w3.org/2003/01/geo/wgs84_pos", "@prefix": true }, + "xsd": "http://www.w3.org/2001/XMLSchema#", "@vocab": "https://w3id.org/biolink/vocab/", "active_in": { "@type": "@id", @@ -644,11 +644,12 @@ "@id": "affects_response_to" }, "affiliation": { - "@type": "xsd:anyURI", + "@type": "@id", "@id": "affiliation" }, "agent_type": { "@context": { + "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -732,6 +733,7 @@ }, "available_from": { "@context": { + "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -788,11 +790,12 @@ "@id": "catalyzes" }, "category": { - "@type": "xsd:anyURI", + "@type": "@id", "@id": "category" }, "causal_mechanism_qualifier": { "@context": { + "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -826,6 +829,7 @@ }, "clinical_approval_status": { "@context": { + "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -1022,6 +1026,7 @@ }, "drug_regulatory_status_world_wide": { "@context": { + "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -1087,6 +1092,7 @@ }, "FDA_adverse_event_level": { "@context": { + "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -1140,6 +1146,7 @@ }, "genome_build": { "@context": { + "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -1459,6 +1466,7 @@ }, "highest_FDA_approval_status": { "@context": { + "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -1632,6 +1640,7 @@ }, "knowledge_level": { "@context": { + "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -1690,6 +1699,7 @@ }, "logical_interpretation": { "@context": { + "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -1709,6 +1719,7 @@ }, "max_research_phase": { "@context": { + "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -1735,7 +1746,7 @@ "@id": "mentions" }, "mesh_terms": { - "@type": "xsd:anyURI", + "@type": "@id", "@id": "mesh_terms" }, "missing_from": { @@ -1816,6 +1827,7 @@ }, "object_direction_qualifier": { "@context": { + "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -1862,7 +1874,7 @@ "@id": "original_object" }, "original_predicate": { - "@type": "xsd:anyURI", + "@type": "@id", "@id": "original_predicate" }, "original_subject": { @@ -1900,6 +1912,7 @@ }, "phase": { "@context": { + "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -1987,7 +2000,7 @@ "@id": "publications" }, "published_in": { - "@type": "xsd:anyURI", + "@type": "@id", "@id": "published_in" }, "publisher": { @@ -2014,6 +2027,7 @@ }, "reaction_direction": { "@context": { + "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -2022,6 +2036,7 @@ }, "reaction_side": { "@context": { + "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -2076,11 +2091,12 @@ "@id": "resistance_associated_with" }, "resource_id": { - "@type": "xsd:anyURI", + "@type": "@id", "@id": "resource_id" }, "resource_role": { "@context": { + "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -2112,6 +2128,7 @@ }, "routes_of_delivery": { "@context": { + "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -2184,6 +2201,7 @@ }, "strand": { "@context": { + "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -2224,6 +2242,7 @@ }, "subject_direction_qualifier": { "@context": { + "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -2274,7 +2293,7 @@ "@id": "supporting_document_year" }, "supporting_documents": { - "@type": "xsd:anyURI", + "@type": "@id", "@id": "supporting_documents" }, "supporting_study_cohort": { @@ -2290,11 +2309,11 @@ "@id": "supporting_study_metadata" }, "supporting_study_method_description": { - "@type": "xsd:anyURI", + "@type": "@id", "@id": "supporting_study_method_description" }, "supporting_study_method_type": { - "@type": "xsd:anyURI", + "@type": "@id", "@id": "supporting_study_method_type" }, "supporting_study_size": { @@ -2399,7 +2418,7 @@ "@id": "update_date" }, "upstream_resource_ids": { - "@type": "xsd:anyURI", + "@type": "@id", "@id": "upstream_resource_ids" }, "url": { @@ -2424,7 +2443,7 @@ "@id": "xenologous_to" }, "xref": { - "@type": "xsd:anyURI", + "@type": "@id", "@id": "xref" }, "AccessibleDnaRegion": { diff --git a/project/jsonld/biolink_model.jsonld b/project/jsonld/biolink_model.jsonld index fe5ad71a2..e691e6da5 100644 --- a/project/jsonld/biolink_model.jsonld +++ b/project/jsonld/biolink_model.jsonld @@ -2058,12 +2058,12 @@ ], "domain": "Entity", "slot_uri": "https://w3id.org/biolink/vocab/has_attribute", + "multivalued": true, "owner": "Entity", "domain_of": [ "Entity" ], "range": "Attribute", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -2123,13 +2123,13 @@ ], "domain": "Attribute", "slot_uri": "https://w3id.org/biolink/vocab/has_quantitative_value", + "multivalued": true, "owner": "ChemicalExposure", "domain_of": [ "Attribute", "ChemicalExposure" ], "range": "QuantityValue", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -2271,12 +2271,12 @@ ], "domain": "Entity", "slot_uri": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "multivalued": true, "owner": "Entity", "domain_of": [ "Entity" ], "range": "string", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -2290,6 +2290,7 @@ "is_a": "type", "domain": "Entity", "slot_uri": "https://w3id.org/biolink/vocab/category", + "multivalued": true, "designates_type": true, "owner": "Entity", "domain_of": [ @@ -2297,7 +2298,6 @@ ], "is_class_field": true, "range": "uriorcurie", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -2316,12 +2316,12 @@ "WIKIDATA" ], "slot_uri": "http://purl.org/dc/terms/type", + "multivalued": true, "owner": "Publication", "domain_of": [ "Publication" ], "range": "string", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -2461,13 +2461,13 @@ "is_a": "node_property", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/synonym", + "multivalued": true, "owner": "GeneProductMixin", "domain_of": [ "NamedThing", "GeneProductMixin" ], "range": "label_type", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -2480,9 +2480,9 @@ "is_a": "synonym", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/exact_synonym", + "multivalued": true, "owner": "exact_synonym", "range": "label_type", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -2495,9 +2495,9 @@ "is_a": "synonym", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/broad_synonym", + "multivalued": true, "owner": "broad_synonym", "range": "label_type", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -2510,9 +2510,9 @@ "is_a": "synonym", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/narrow_synonym", + "multivalued": true, "owner": "narrow_synonym", "range": "label_type", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -2525,9 +2525,9 @@ "is_a": "synonym", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/related_synonym", + "multivalued": true, "owner": "related_synonym", "range": "label_type", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -2586,6 +2586,7 @@ ], "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/xref", + "multivalued": true, "owner": "GeneProductMixin", "domain_of": [ "NamedThing", @@ -2595,7 +2596,6 @@ "GeneProductMixin" ], "range": "uriorcurie", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -2636,9 +2636,9 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/support_graphs", + "multivalued": true, "owner": "support_graphs", "range": "string", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -2686,12 +2686,12 @@ ], "from_schema": "https://w3id.org/biolink/biolink-model", "slot_uri": "https://w3id.org/biolink/vocab/retrieval_source_ids", + "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "RetrievalSource", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -2764,9 +2764,9 @@ "is_a": "node_property", "domain": "NamedThing", "slot_uri": "http://purl.obolibrary.org/obo/go#systematic_synonym", + "multivalued": true, "owner": "systematic_synonym", "range": "label_type", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -2777,12 +2777,12 @@ "is_a": "node_property", "domain": "Agent", "slot_uri": "https://w3id.org/biolink/vocab/affiliation", + "multivalued": true, "owner": "Agent", "domain_of": [ "Agent" ], "range": "uriorcurie", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -3272,12 +3272,12 @@ "is_a": "node_property", "domain": "Publication", "slot_uri": "https://w3id.org/biolink/vocab/authors", + "multivalued": true, "owner": "Publication", "domain_of": [ "Publication" ], "range": "Agent", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -3348,12 +3348,12 @@ "is_a": "node_property", "domain": "Publication", "slot_uri": "https://w3id.org/biolink/vocab/pages", + "multivalued": true, "owner": "Publication", "domain_of": [ "Publication" ], "range": "string", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -3386,12 +3386,12 @@ "is_a": "node_property", "domain": "Publication", "slot_uri": "https://w3id.org/biolink/vocab/keywords", + "multivalued": true, "owner": "Publication", "domain_of": [ "Publication" ], "range": "string", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -3408,12 +3408,12 @@ ], "domain": "Publication", "slot_uri": "https://w3id.org/biolink/vocab/mesh_terms", + "multivalued": true, "owner": "Publication", "domain_of": [ "Publication" ], "range": "uriorcurie", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -3440,12 +3440,12 @@ "is_a": "node_property", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_gene_or_gene_product", + "multivalued": true, "owner": "GeneGroupingMixin", "domain_of": [ "GeneGroupingMixin" ], "range": "Gene", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -3456,12 +3456,12 @@ "is_a": "has_gene_or_gene_product", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_gene", + "multivalued": true, "owner": "SequenceVariant", "domain_of": [ "SequenceVariant" ], "range": "Gene", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -3519,9 +3519,9 @@ "is_a": "node_property", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_constituent", + "multivalued": true, "owner": "has_constituent", "range": "MolecularEntity", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -3532,12 +3532,12 @@ "is_a": "node_property", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_drug", + "multivalued": true, "owner": "Treatment", "domain_of": [ "Treatment" ], "range": "Drug", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -3548,12 +3548,12 @@ "is_a": "node_property", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_device", + "multivalued": true, "owner": "Treatment", "domain_of": [ "Treatment" ], "range": "Device", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -3564,12 +3564,12 @@ "is_a": "node_property", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_procedure", + "multivalued": true, "owner": "Treatment", "domain_of": [ "Treatment" ], "range": "Procedure", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -3706,12 +3706,12 @@ "is_a": "node_property", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/available_from", + "multivalued": true, "owner": "ChemicalEntity", "domain_of": [ "ChemicalEntity" ], "range": "DrugAvailabilityEnum", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -3743,13 +3743,13 @@ "is_a": "related_to_at_concept_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_chemical_role", + "multivalued": true, "inherited": true, "owner": "ChemicalEntity", "domain_of": [ "ChemicalEntity" ], "range": "ChemicalRole", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -3775,9 +3775,9 @@ "is_a": "node_property", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/animal_model_available_from", + "multivalued": true, "owner": "animal_model_available_from", "range": "DiseaseOrPhenotypicFeature", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -3856,12 +3856,12 @@ "description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "from_schema": "https://w3id.org/biolink/biolink-model", "slot_uri": "https://w3id.org/biolink/vocab/routes_of_delivery", + "multivalued": true, "owner": "ChemicalMixture", "domain_of": [ "ChemicalMixture" ], "range": "DrugDeliveryEnum", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -4054,12 +4054,12 @@ "description": "A collection of relationships that are not used in biolink, but have biolink patterns that can be used to replace them. This is a temporary slot to help with the transition to the fully qualified predicate model in Biolink3.", "from_schema": "https://w3id.org/biolink/biolink-model", "slot_uri": "https://w3id.org/biolink/vocab/predicate_mappings", + "multivalued": true, "owner": "MappingCollection", "domain_of": [ "MappingCollection" ], "range": "PredicateMapping", - "multivalued": true, "inlined": true, "inlined_as_list": true, "@type": "SlotDefinition" @@ -4070,8 +4070,8 @@ "description": "A list of terms from different schemas or terminology systems that have an identical meaning. Such terms often describe the same concept from different ontological perspectives.", "from_schema": "https://w3id.org/biolink/biolink-model", "slot_uri": "https://w3id.org/biolink/vocab/exact_matches", - "range": "string", "multivalued": true, + "range": "string", "@type": "SlotDefinition" }, { @@ -4080,8 +4080,8 @@ "description": "A list of terms from different schemas or terminology systems that have a narrower meaning. Such terms often describe a more specific concept from different ontological perspectives.", "from_schema": "https://w3id.org/biolink/biolink-model", "slot_uri": "https://w3id.org/biolink/vocab/narrow_matches", - "range": "string", "multivalued": true, + "range": "string", "@type": "SlotDefinition" }, { @@ -4090,8 +4090,8 @@ "description": "A list of terms from different schemas or terminology systems that have a broader meaning. Such terms often describe a more general concept from different ontological perspectives.", "from_schema": "https://w3id.org/biolink/biolink-model", "slot_uri": "https://w3id.org/biolink/vocab/broad_matches", - "range": "string", "multivalued": true, + "range": "string", "@type": "SlotDefinition" }, { @@ -4590,12 +4590,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/qualifiers", + "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "OntologyClass", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -4727,12 +4727,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/catalyst_qualifier", + "multivalued": true, "owner": "ChemicalToChemicalDerivationAssociation", "domain_of": [ "ChemicalToChemicalDerivationAssociation" ], "range": "MacromolecularMachineMixin", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -4891,11 +4891,11 @@ ], "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/related_to", + "multivalued": true, "inherited": true, "owner": "related_to", "symmetric": true, "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -4913,11 +4913,11 @@ "is_a": "related_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/related_to_at_concept_level", + "multivalued": true, "inherited": true, "owner": "related_to_at_concept_level", "symmetric": true, "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -4935,11 +4935,11 @@ "is_a": "related_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/related_to_at_instance_level", + "multivalued": true, "inherited": true, "owner": "related_to_at_instance_level", "symmetric": true, "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -4961,11 +4961,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/associated_with", + "multivalued": true, "inherited": true, "owner": "associated_with", "symmetric": true, "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -4995,11 +4995,11 @@ "is_a": "related_to_at_concept_level", "domain": "OntologyClass", "slot_uri": "https://w3id.org/biolink/vocab/superclass_of", + "multivalued": true, "inherited": true, "owner": "superclass_of", "inverse": "subclass_of", "range": "OntologyClass", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5053,11 +5053,11 @@ "is_a": "related_to_at_concept_level", "domain": "OntologyClass", "slot_uri": "https://w3id.org/biolink/vocab/subclass_of", + "multivalued": true, "inherited": true, "owner": "subclass_of", "inverse": "superclass_of", "range": "OntologyClass", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5091,11 +5091,11 @@ "is_a": "exact_match", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/same_as", + "multivalued": true, "inherited": true, "owner": "same_as", "symmetric": true, "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5128,11 +5128,11 @@ "is_a": "related_to_at_concept_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/close_match", + "multivalued": true, "inherited": true, "owner": "close_match", "symmetric": true, "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5158,6 +5158,7 @@ "is_a": "close_match", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/exact_match", + "multivalued": true, "inherited": true, "owner": "PredicateMapping", "domain_of": [ @@ -5165,7 +5166,6 @@ ], "symmetric": true, "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5195,6 +5195,7 @@ "is_a": "related_to_at_concept_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/broad_match", + "multivalued": true, "inherited": true, "owner": "PredicateMapping", "domain_of": [ @@ -5202,7 +5203,6 @@ ], "inverse": "narrow_match", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5227,6 +5227,7 @@ "is_a": "related_to_at_concept_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/narrow_match", + "multivalued": true, "inherited": true, "owner": "PredicateMapping", "domain_of": [ @@ -5234,7 +5235,6 @@ ], "inverse": "broad_match", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5254,11 +5254,11 @@ "is_a": "related_to_at_concept_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/member_of", + "multivalued": true, "inherited": true, "owner": "member_of", "inverse": "has_member", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5276,11 +5276,11 @@ "is_a": "related_to_at_concept_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_member", + "multivalued": true, "inherited": true, "owner": "has_member", "inverse": "member_of", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5305,11 +5305,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/opposite_of", + "multivalued": true, "inherited": true, "owner": "opposite_of", "symmetric": true, "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5333,11 +5333,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/affects_likelihood_of", + "multivalued": true, "inherited": true, "owner": "affects_likelihood_of", "inverse": "likelihood_affected_by", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5347,11 +5347,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/likelihood_affected_by", + "multivalued": true, "inherited": true, "owner": "likelihood_affected_by", "inverse": "affects_likelihood_of", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5369,11 +5369,11 @@ "is_a": "associated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/associated_with_likelihood_of", + "multivalued": true, "inherited": true, "owner": "associated_with_likelihood_of", "inverse": "likelihood_associated_with", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5384,11 +5384,11 @@ "is_a": "associated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/likelihood_associated_with", + "multivalued": true, "inherited": true, "owner": "likelihood_associated_with", "inverse": "associated_with_likelihood_of", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5406,11 +5406,11 @@ "is_a": "associated_with_likelihood_of", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/associated_with_increased_likelihood_of", + "multivalued": true, "inherited": true, "owner": "associated_with_increased_likelihood_of", "inverse": "increased_likelihood_associated_with", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5421,11 +5421,11 @@ "is_a": "likelihood_associated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/increased_likelihood_associated_with", + "multivalued": true, "inherited": true, "owner": "increased_likelihood_associated_with", "inverse": "associated_with_increased_likelihood_of", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5443,11 +5443,11 @@ "is_a": "associated_with_likelihood_of", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/associated_with_decreased_likelihood_of", + "multivalued": true, "inherited": true, "owner": "associated_with_decreased_likelihood_of", "inverse": "decreased_likelihood_associated_with", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5458,11 +5458,11 @@ "is_a": "likelihood_associated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/decreased_likelihood_associated_with", + "multivalued": true, "inherited": true, "owner": "decreased_likelihood_associated_with", "inverse": "associated_with_decreased_likelihood_of", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5480,11 +5480,11 @@ "is_a": "related_to_at_instance_level", "domain": "Gene", "slot_uri": "https://w3id.org/biolink/vocab/target_for", + "multivalued": true, "inherited": true, "owner": "target_for", "inverse": "has_target", "range": "Disease", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5494,11 +5494,11 @@ "is_a": "related_to_at_instance_level", "domain": "Disease", "slot_uri": "https://w3id.org/biolink/vocab/has_target", + "multivalued": true, "inherited": true, "owner": "has_target", "inverse": "target_for", "range": "Gene", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5518,11 +5518,11 @@ "is_a": "related_to_at_instance_level", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/active_in", + "multivalued": true, "inherited": true, "owner": "active_in", "inverse": "has_active_component", "range": "CellularComponent", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5532,11 +5532,11 @@ "is_a": "related_to_at_instance_level", "domain": "CellularComponent", "slot_uri": "https://w3id.org/biolink/vocab/has_active_component", + "multivalued": true, "inherited": true, "owner": "has_active_component", "inverse": "active_in", "range": "GeneOrGeneProduct", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -5557,11 +5557,11 @@ "is_a": "related_to_at_instance_level", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/acts_upstream_of", + "multivalued": true, "inherited": true, "owner": "acts_upstream_of", "inverse": "has_upstream_actor", "range": "BiologicalProcess", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5571,11 +5571,11 @@ "is_a": "related_to_at_instance_level", "domain": "BiologicalProcess", "slot_uri": "https://w3id.org/biolink/vocab/has_upstream_actor", + "multivalued": true, "inherited": true, "owner": "has_upstream_actor", "inverse": "acts_upstream_of", "range": "GeneOrGeneProduct", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -5596,11 +5596,11 @@ "is_a": "acts_upstream_of", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/acts_upstream_of_positive_effect", + "multivalued": true, "inherited": true, "owner": "acts_upstream_of_positive_effect", "inverse": "has_positive_upstream_actor", "range": "BiologicalProcess", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5610,11 +5610,11 @@ "is_a": "has_upstream_actor", "domain": "BiologicalProcess", "slot_uri": "https://w3id.org/biolink/vocab/has_positive_upstream_actor", + "multivalued": true, "inherited": true, "owner": "has_positive_upstream_actor", "inverse": "acts_upstream_of_positive_effect", "range": "GeneOrGeneProduct", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -5635,11 +5635,11 @@ "is_a": "acts_upstream_of", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/acts_upstream_of_negative_effect", + "multivalued": true, "inherited": true, "owner": "acts_upstream_of_negative_effect", "inverse": "has_negative_upstream_actor", "range": "BiologicalProcess", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5649,11 +5649,11 @@ "is_a": "has_upstream_actor", "domain": "BiologicalProcess", "slot_uri": "https://w3id.org/biolink/vocab/has_negative_upstream_actor", + "multivalued": true, "inherited": true, "owner": "has_negative_upstream_actor", "inverse": "acts_upstream_of_negative_effect", "range": "GeneOrGeneProduct", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -5674,11 +5674,11 @@ "is_a": "acts_upstream_of", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/acts_upstream_of_or_within", + "multivalued": true, "inherited": true, "owner": "acts_upstream_of_or_within", "inverse": "has_upstream_or_within_actor", "range": "BiologicalProcess", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5688,11 +5688,11 @@ "is_a": "has_upstream_actor", "domain": "BiologicalProcess", "slot_uri": "https://w3id.org/biolink/vocab/has_upstream_or_within_actor", + "multivalued": true, "inherited": true, "owner": "has_upstream_or_within_actor", "inverse": "acts_upstream_of_or_within", "range": "GeneOrGeneProduct", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -5713,11 +5713,11 @@ "is_a": "acts_upstream_of_or_within", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/acts_upstream_of_or_within_positive_effect", + "multivalued": true, "inherited": true, "owner": "acts_upstream_of_or_within_positive_effect", "inverse": "has_positive_upstream_or_within_actor", "range": "BiologicalProcess", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5727,11 +5727,11 @@ "is_a": "has_upstream_or_within_actor", "domain": "BiologicalProcess", "slot_uri": "https://w3id.org/biolink/vocab/has_positive_upstream_or_within_actor", + "multivalued": true, "inherited": true, "owner": "has_positive_upstream_or_within_actor", "inverse": "acts_upstream_of_or_within_positive_effect", "range": "GeneOrGeneProduct", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -5752,11 +5752,11 @@ "is_a": "acts_upstream_of_or_within", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/acts_upstream_of_or_within_negative_effect", + "multivalued": true, "inherited": true, "owner": "acts_upstream_of_or_within_negative_effect", "inverse": "has_negative_upstream_or_within_actor", "range": "BiologicalProcess", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5766,11 +5766,11 @@ "is_a": "has_upstream_or_within_actor", "domain": "BiologicalProcess", "slot_uri": "https://w3id.org/biolink/vocab/has_negative_upstream_or_within_actor", + "multivalued": true, "inherited": true, "owner": "has_negative_upstream_or_within_actor", "inverse": "acts_upstream_of_or_within_negative_effect", "range": "GeneOrGeneProduct", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -5788,11 +5788,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/mentions", + "multivalued": true, "inherited": true, "owner": "mentions", "inverse": "mentioned_by", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5803,11 +5803,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/mentioned_by", + "multivalued": true, "inherited": true, "owner": "mentioned_by", "inverse": "mentions", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5824,11 +5824,11 @@ "abstract": true, "domain": "Agent", "slot_uri": "https://w3id.org/biolink/vocab/contributor", + "multivalued": true, "inherited": true, "owner": "contributor", "inverse": "has_contributor", "range": "InformationContentEntity", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5838,11 +5838,11 @@ "is_a": "related_to_at_instance_level", "domain": "InformationContentEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_contributor", + "multivalued": true, "inherited": true, "owner": "has_contributor", "inverse": "contributor", "range": "Agent", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5853,11 +5853,11 @@ "is_a": "contributor", "domain": "Agent", "slot_uri": "https://w3id.org/biolink/vocab/provider", + "multivalued": true, "inherited": true, "owner": "provider", "inverse": "has_provider", "range": "InformationContentEntity", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5867,11 +5867,11 @@ "is_a": "has_contributor", "domain": "InformationContentEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_provider", + "multivalued": true, "inherited": true, "owner": "has_provider", "inverse": "provider", "range": "Agent", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5886,11 +5886,11 @@ "is_a": "contributor", "domain": "Agent", "slot_uri": "https://w3id.org/biolink/vocab/publisher", + "multivalued": true, "inherited": true, "owner": "publisher", "inverse": "has_publisher", "range": "Publication", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5900,11 +5900,11 @@ "is_a": "has_contributor", "domain": "Publication", "slot_uri": "https://w3id.org/biolink/vocab/has_publisher", + "multivalued": true, "inherited": true, "owner": "has_publisher", "inverse": "publisher", "range": "Agent", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5918,11 +5918,11 @@ "is_a": "contributor", "domain": "Agent", "slot_uri": "https://w3id.org/biolink/vocab/editor", + "multivalued": true, "inherited": true, "owner": "editor", "inverse": "has_editor", "range": "Publication", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5932,11 +5932,11 @@ "is_a": "has_contributor", "domain": "Publication", "slot_uri": "https://w3id.org/biolink/vocab/has_editor", + "multivalued": true, "inherited": true, "owner": "has_editor", "inverse": "editor", "range": "Agent", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5951,11 +5951,11 @@ "is_a": "contributor", "domain": "Agent", "slot_uri": "https://w3id.org/biolink/vocab/author", + "multivalued": true, "inherited": true, "owner": "author", "inverse": "has_author", "range": "Publication", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5965,11 +5965,11 @@ "is_a": "has_contributor", "domain": "Publication", "slot_uri": "https://w3id.org/biolink/vocab/has_author", + "multivalued": true, "inherited": true, "owner": "has_author", "inverse": "author", "range": "Agent", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -5990,11 +5990,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/assesses", + "multivalued": true, "inherited": true, "owner": "assesses", "inverse": "is_assessed_by", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -6004,11 +6004,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/is_assessed_by", + "multivalued": true, "inherited": true, "owner": "is_assessed_by", "inverse": "assesses", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -6029,11 +6029,11 @@ "mixin": true, "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/interacts_with", + "multivalued": true, "inherited": true, "owner": "interacts_with", "symmetric": true, "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -6075,11 +6075,11 @@ ], "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/physically_interacts_with", + "multivalued": true, "inherited": true, "owner": "physically_interacts_with", "symmetric": true, "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -6110,11 +6110,11 @@ "is_a": "physically_interacts_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/directly_physically_interacts_with", + "multivalued": true, "inherited": true, "owner": "directly_physically_interacts_with", "symmetric": true, "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -6136,11 +6136,11 @@ "is_a": "directly_physically_interacts_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/binds", + "multivalued": true, "inherited": true, "owner": "binds", "symmetric": true, "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -6157,11 +6157,11 @@ "is_a": "physically_interacts_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/indirectly_physically_interacts_with", + "multivalued": true, "inherited": true, "owner": "indirectly_physically_interacts_with", "symmetric": true, "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -6185,11 +6185,11 @@ "is_a": "interacts_with", "domain": "Gene", "slot_uri": "https://w3id.org/biolink/vocab/genetically_interacts_with", + "multivalued": true, "inherited": true, "owner": "genetically_interacts_with", "symmetric": true, "range": "Gene", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -6210,11 +6210,11 @@ "is_a": "genetically_interacts_with", "domain": "Gene", "slot_uri": "https://w3id.org/biolink/vocab/gene_fusion_with", + "multivalued": true, "inherited": true, "owner": "gene_fusion_with", "symmetric": true, "range": "Gene", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -6235,11 +6235,11 @@ "is_a": "genetically_interacts_with", "domain": "Gene", "slot_uri": "https://w3id.org/biolink/vocab/genetic_neighborhood_of", + "multivalued": true, "inherited": true, "owner": "genetic_neighborhood_of", "symmetric": true, "range": "Gene", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -6302,11 +6302,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/affects", + "multivalued": true, "inherited": true, "owner": "affects", "inverse": "affected_by", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -6317,11 +6317,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/affected_by", + "multivalued": true, "inherited": true, "owner": "affected_by", "inverse": "affects", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -6345,11 +6345,11 @@ "is_a": "associated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/associated_with_sensitivity_to", + "multivalued": true, "inherited": true, "owner": "associated_with_sensitivity_to", "inverse": "sensitivity_associated_with", "range": "ChemicalEntity", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -6359,11 +6359,11 @@ "is_a": "associated_with", "domain": "ChemicalEntity", "slot_uri": "https://w3id.org/biolink/vocab/sensitivity_associated_with", + "multivalued": true, "inherited": true, "owner": "sensitivity_associated_with", "inverse": "associated_with_sensitivity_to", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -6381,11 +6381,11 @@ "is_a": "associated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/associated_with_resistance_to", + "multivalued": true, "inherited": true, "owner": "associated_with_resistance_to", "inverse": "resistance_associated_with", "range": "ChemicalEntity", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -6395,11 +6395,11 @@ "is_a": "associated_with", "domain": "ChemicalEntity", "slot_uri": "https://w3id.org/biolink/vocab/resistance_associated_with", + "multivalued": true, "inherited": true, "owner": "resistance_associated_with", "inverse": "associated_with_resistance_to", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -6425,11 +6425,11 @@ "is_a": "related_to_at_instance_level", "domain": "DiagnosticAid", "slot_uri": "https://w3id.org/biolink/vocab/diagnoses", + "multivalued": true, "inherited": true, "owner": "diagnoses", "inverse": "is_diagnosed_by", "range": "DiseaseOrPhenotypicFeature", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -6439,11 +6439,11 @@ "is_a": "related_to_at_instance_level", "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/is_diagnosed_by", + "multivalued": true, "inherited": true, "owner": "is_diagnosed_by", "inverse": "diagnoses", "range": "DiagnosticAid", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -6456,11 +6456,11 @@ "mixin": true, "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/increases_amount_or_activity_of", + "multivalued": true, "inherited": true, "owner": "increases_amount_or_activity_of", "inverse": "amount_or_activity_increased_by", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -6471,11 +6471,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/amount_or_activity_increased_by", + "multivalued": true, "inherited": true, "owner": "amount_or_activity_increased_by", "inverse": "increases_amount_or_activity_of", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -6488,11 +6488,11 @@ "mixin": true, "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/decreases_amount_or_activity_of", + "multivalued": true, "inherited": true, "owner": "decreases_amount_or_activity_of", "inverse": "amount_or_activity_decreased_by", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -6503,11 +6503,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/amount_or_activity_decreased_by", + "multivalued": true, "inherited": true, "owner": "amount_or_activity_decreased_by", "inverse": "decreases_amount_or_activity_of", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -6556,11 +6556,11 @@ "is_a": "affects", "domain": "ChemicalEntityOrGeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/affects_response_to", + "multivalued": true, "inherited": true, "owner": "affects_response_to", "inverse": "response_affected_by", "range": "ChemicalEntityOrGeneOrGeneProduct", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -6575,11 +6575,11 @@ "is_a": "affected_by", "domain": "ChemicalEntityOrGeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/response_affected_by", + "multivalued": true, "inherited": true, "owner": "response_affected_by", "inverse": "affects_response_to", "range": "ChemicalEntityOrGeneOrGeneProduct", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -6609,11 +6609,11 @@ "is_a": "affects_response_to", "domain": "ChemicalEntityOrGeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/increases_response_to", + "multivalued": true, "inherited": true, "owner": "increases_response_to", "inverse": "response_increased_by", "range": "ChemicalEntityOrGeneOrGeneProduct", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -6627,11 +6627,11 @@ "is_a": "response_affected_by", "domain": "ChemicalEntityOrGeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/response_increased_by", + "multivalued": true, "inherited": true, "owner": "response_increased_by", "inverse": "increases_response_to", "range": "ChemicalEntityOrGeneOrGeneProduct", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -6664,11 +6664,11 @@ "is_a": "affects_response_to", "domain": "ChemicalEntityOrGeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/decreases_response_to", + "multivalued": true, "inherited": true, "owner": "decreases_response_to", "inverse": "response_decreased_by", "range": "ChemicalEntityOrGeneOrGeneProduct", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -6682,11 +6682,11 @@ "is_a": "response_affected_by", "domain": "ChemicalEntityOrGeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/response_decreased_by", + "multivalued": true, "inherited": true, "owner": "response_decreased_by", "inverse": "decreases_response_to", "range": "ChemicalEntityOrGeneOrGeneProduct", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -6721,11 +6721,11 @@ ], "domain": "PhysicalEssenceOrOccurrent", "slot_uri": "https://w3id.org/biolink/vocab/regulates", + "multivalued": true, "inherited": true, "owner": "regulates", "inverse": "regulated_by", "range": "PhysicalEssenceOrOccurrent", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -6736,11 +6736,11 @@ "is_a": "affected_by", "domain": "PhysicalEssenceOrOccurrent", "slot_uri": "https://w3id.org/biolink/vocab/regulated_by", + "multivalued": true, "inherited": true, "owner": "regulated_by", "inverse": "regulates", "range": "PhysicalEssenceOrOccurrent", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -6778,11 +6778,11 @@ "is_a": "affects", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/disrupts", + "multivalued": true, "inherited": true, "owner": "disrupts", "inverse": "disrupted_by", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -6793,11 +6793,11 @@ "is_a": "affected_by", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/disrupted_by", + "multivalued": true, "inherited": true, "owner": "disrupted_by", "inverse": "disrupts", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -6821,11 +6821,11 @@ "is_a": "related_to_at_instance_level", "domain": "GeneProductMixin", "slot_uri": "https://w3id.org/biolink/vocab/gene_product_of", + "multivalued": true, "inherited": true, "owner": "gene_product_of", "inverse": "has_gene_product", "range": "Gene", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -6850,11 +6850,11 @@ "is_a": "related_to_at_instance_level", "domain": "Gene", "slot_uri": "https://w3id.org/biolink/vocab/has_gene_product", + "multivalued": true, "inherited": true, "owner": "has_gene_product", "inverse": "gene_product_of", "range": "GeneProductMixin", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -6870,11 +6870,11 @@ "is_a": "related_to_at_instance_level", "domain": "Gene", "slot_uri": "https://w3id.org/biolink/vocab/transcribed_to", + "multivalued": true, "inherited": true, "owner": "transcribed_to", "inverse": "transcribed_from", "range": "Transcript", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -6896,11 +6896,11 @@ "is_a": "related_to_at_instance_level", "domain": "Transcript", "slot_uri": "https://w3id.org/biolink/vocab/transcribed_from", + "multivalued": true, "inherited": true, "owner": "transcribed_from", "inverse": "transcribed_to", "range": "Gene", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -6922,11 +6922,11 @@ "is_a": "related_to_at_instance_level", "domain": "Transcript", "slot_uri": "https://w3id.org/biolink/vocab/translates_to", + "multivalued": true, "inherited": true, "owner": "translates_to", "inverse": "translation_of", "range": "Protein", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -6941,11 +6941,11 @@ "is_a": "related_to_at_instance_level", "domain": "Protein", "slot_uri": "https://w3id.org/biolink/vocab/translation_of", + "multivalued": true, "inherited": true, "owner": "translation_of", "inverse": "translates_to", "range": "Transcript", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -6979,11 +6979,11 @@ "is_a": "similar_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/homologous_to", + "multivalued": true, "inherited": true, "owner": "homologous_to", "symmetric": true, "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -7007,11 +7007,11 @@ "is_a": "homologous_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/paralogous_to", + "multivalued": true, "inherited": true, "owner": "paralogous_to", "symmetric": true, "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -7036,11 +7036,11 @@ "is_a": "homologous_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/orthologous_to", + "multivalued": true, "inherited": true, "owner": "orthologous_to", "symmetric": true, "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -7064,11 +7064,11 @@ "is_a": "homologous_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/xenologous_to", + "multivalued": true, "inherited": true, "owner": "xenologous_to", "symmetric": true, "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -7260,11 +7260,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/coexists_with", + "multivalued": true, "inherited": true, "owner": "coexists_with", "symmetric": true, "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -7288,11 +7288,11 @@ "is_a": "coexists_with", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/in_pathway_with", + "multivalued": true, "inherited": true, "owner": "in_pathway_with", "symmetric": true, "range": "GeneOrGeneProduct", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -7320,11 +7320,11 @@ "is_a": "coexists_with", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/in_complex_with", + "multivalued": true, "inherited": true, "owner": "in_complex_with", "symmetric": true, "range": "GeneOrGeneProduct", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -7346,11 +7346,11 @@ "is_a": "coexists_with", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/in_cell_population_with", + "multivalued": true, "inherited": true, "owner": "in_cell_population_with", "symmetric": true, "range": "GeneOrGeneProduct", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -7375,11 +7375,11 @@ "is_a": "coexists_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/colocalizes_with", + "multivalued": true, "inherited": true, "owner": "colocalizes_with", "symmetric": true, "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -7391,11 +7391,11 @@ "is_a": "associated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/genetic_association", + "multivalued": true, "inherited": true, "owner": "genetic_association", "symmetric": true, "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -7424,11 +7424,11 @@ "is_a": "associated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/genetically_associated_with", + "multivalued": true, "inherited": true, "owner": "genetically_associated_with", "symmetric": true, "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -7458,11 +7458,11 @@ "is_a": "genetically_associated_with", "domain": "Gene", "slot_uri": "https://w3id.org/biolink/vocab/gene_associated_with_condition", + "multivalued": true, "inherited": true, "owner": "gene_associated_with_condition", "inverse": "condition_associated_with_gene", "range": "DiseaseOrPhenotypicFeature", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -7483,11 +7483,11 @@ "is_a": "genetically_associated_with", "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/condition_associated_with_gene", + "multivalued": true, "inherited": true, "owner": "condition_associated_with_gene", "inverse": "gene_associated_with_condition", "range": "Gene", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -7520,11 +7520,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/contributes_to", + "multivalued": true, "inherited": true, "owner": "contributes_to", "inverse": "contribution_from", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -7537,11 +7537,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/contribution_from", + "multivalued": true, "inherited": true, "owner": "contribution_from", "inverse": "contributes_to", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -7598,11 +7598,11 @@ "is_a": "contributes_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/causes", + "multivalued": true, "inherited": true, "owner": "causes", "inverse": "caused_by", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -7633,11 +7633,11 @@ "is_a": "contribution_from", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/caused_by", + "multivalued": true, "inherited": true, "owner": "caused_by", "inverse": "causes", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -7674,11 +7674,11 @@ ], "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/ameliorates_condition", + "multivalued": true, "inherited": true, "owner": "ameliorates_condition", "inverse": "condition_ameliorated_by", "range": "DiseaseOrPhenotypicFeature", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -7688,11 +7688,11 @@ "is_a": "affected_by", "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/condition_ameliorated_by", + "multivalued": true, "inherited": true, "owner": "condition_ameliorated_by", "inverse": "ameliorates_condition", "range": "ChemicalOrDrugOrTreatment", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -7729,11 +7729,11 @@ ], "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/preventative_for_condition", + "multivalued": true, "inherited": true, "owner": "preventative_for_condition", "inverse": "condition_prevented_by", "range": "DiseaseOrPhenotypicFeature", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -7743,11 +7743,11 @@ "is_a": "affected_by", "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/condition_prevented_by", + "multivalued": true, "inherited": true, "owner": "condition_prevented_by", "inverse": "preventative_for_condition", "range": "ChemicalOrDrugOrTreatment", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -7775,11 +7775,11 @@ "mixin": true, "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/promotes_condition", + "multivalued": true, "inherited": true, "owner": "promotes_condition", "inverse": "condition_promoted_by", "range": "DiseaseOrPhenotypicFeature", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -7790,11 +7790,11 @@ "mixin": true, "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/condition_promoted_by", + "multivalued": true, "inherited": true, "owner": "condition_promoted_by", "inverse": "promotes_condition", "range": "ChemicalOrDrugOrTreatment", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -7825,11 +7825,11 @@ ], "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/predisposes_to_condition", + "multivalued": true, "inherited": true, "owner": "predisposes_to_condition", "inverse": "condition_predisposed_by", "range": "DiseaseOrPhenotypicFeature", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -7839,11 +7839,11 @@ "is_a": "likelihood_affected_by", "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/condition_predisposed_by", + "multivalued": true, "inherited": true, "owner": "condition_predisposed_by", "inverse": "predisposes_to_condition", "range": "ChemicalOrDrugOrTreatment", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -7880,11 +7880,11 @@ ], "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/exacerbates_condition", + "multivalued": true, "inherited": true, "owner": "exacerbates_condition", "inverse": "condition_exacerbated_by", "range": "DiseaseOrPhenotypicFeature", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -7897,11 +7897,11 @@ "is_a": "affected_by", "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/condition_exacerbated_by", + "multivalued": true, "inherited": true, "owner": "condition_exacerbated_by", "inverse": "exacerbates_condition", "range": "ChemicalOrDrugOrTreatment", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -7966,11 +7966,11 @@ "mixin": true, "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/treats", + "multivalued": true, "inherited": true, "owner": "treats", "inverse": "treated_by", "range": "DiseaseOrPhenotypicFeature", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -7991,11 +7991,11 @@ "mixin": true, "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/treated_by", + "multivalued": true, "inherited": true, "owner": "treated_by", "inverse": "treats", "range": "ChemicalOrDrugOrTreatment", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -8020,11 +8020,11 @@ ], "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/studied_to_treat", + "multivalued": true, "inherited": true, "owner": "studied_to_treat", "inverse": "treated_in_studies_by", "range": "DiseaseOrPhenotypicFeature", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -8051,11 +8051,11 @@ ], "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/in_clinical_trials_for", + "multivalued": true, "inherited": true, "owner": "in_clinical_trials_for", "inverse": "tested_by_clinical_trials_of", "range": "DiseaseOrPhenotypicFeature", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -8068,11 +8068,11 @@ ], "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/tested_by_clinical_trials_of", + "multivalued": true, "inherited": true, "owner": "tested_by_clinical_trials_of", "inverse": "in_clinical_trials_for", "range": "ChemicalOrDrugOrTreatment", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -8086,11 +8086,11 @@ ], "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/treated_in_studies_by", + "multivalued": true, "inherited": true, "owner": "treated_in_studies_by", "inverse": "studied_to_treat", "range": "ChemicalOrDrugOrTreatment", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -8104,11 +8104,11 @@ ], "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/tested_by_preclinical_trials_of", + "multivalued": true, "inherited": true, "owner": "tested_by_preclinical_trials_of", "inverse": "in_preclinical_trials_for", "range": "ChemicalOrDrugOrTreatment", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -8133,11 +8133,11 @@ ], "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/in_preclinical_trials_for", + "multivalued": true, "inherited": true, "owner": "in_preclinical_trials_for", "inverse": "tested_by_preclinical_trials_of", "range": "DiseaseOrPhenotypicFeature", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -8164,11 +8164,11 @@ ], "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/beneficial_in_models_for", + "multivalued": true, "inherited": true, "owner": "beneficial_in_models_for", "inverse": "models_demonstrating_benefits_for", "range": "DiseaseOrPhenotypicFeature", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -8181,11 +8181,11 @@ ], "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/models_demonstrating_benefits_for", + "multivalued": true, "inherited": true, "owner": "models_demonstrating_benefits_for", "inverse": "beneficial_in_models_for", "range": "ChemicalOrDrugOrTreatment", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -8218,11 +8218,11 @@ ], "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/applied_to_treat", + "multivalued": true, "inherited": true, "owner": "applied_to_treat", "inverse": "treatment_applications_from", "range": "DiseaseOrPhenotypicFeature", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -8235,11 +8235,11 @@ ], "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/treatment_applications_from", + "multivalued": true, "inherited": true, "owner": "treatment_applications_from", "inverse": "applied_to_treat", "range": "ChemicalOrDrugOrTreatment", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -8268,11 +8268,11 @@ "mixin": true, "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/treats_or_applied_or_studied_to_treat", + "multivalued": true, "inherited": true, "owner": "treats_or_applied_or_studied_to_treat", "inverse": "subject_of_treatment_application_or_study_for_treatment_by", "range": "DiseaseOrPhenotypicFeature", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -8283,11 +8283,11 @@ "mixin": true, "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/subject_of_treatment_application_or_study_for_treatment_by", + "multivalued": true, "inherited": true, "owner": "subject_of_treatment_application_or_study_for_treatment_by", "inverse": "treats_or_applied_or_studied_to_treat", "range": "ChemicalOrDrugOrTreatment", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -8316,11 +8316,11 @@ "is_a": "associated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/correlated_with", + "multivalued": true, "inherited": true, "owner": "correlated_with", "symmetric": true, "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -8349,11 +8349,11 @@ "is_a": "correlated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/positively_correlated_with", + "multivalued": true, "inherited": true, "owner": "positively_correlated_with", "symmetric": true, "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -8382,11 +8382,11 @@ "is_a": "correlated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/negatively_correlated_with", + "multivalued": true, "inherited": true, "owner": "negatively_correlated_with", "symmetric": true, "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -8407,11 +8407,11 @@ "is_a": "correlated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/occurs_together_in_literature_with", + "multivalued": true, "inherited": true, "owner": "occurs_together_in_literature_with", "symmetric": true, "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -8429,11 +8429,11 @@ "is_a": "correlated_with", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/coexpressed_with", + "multivalued": true, "inherited": true, "owner": "coexpressed_with", "symmetric": true, "range": "GeneOrGeneProduct", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -8452,11 +8452,11 @@ "is_a": "correlated_with", "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/has_biomarker", + "multivalued": true, "inherited": true, "owner": "has_biomarker", "inverse": "biomarker_for", "range": "ChemicalEntityOrGeneOrGeneProduct", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -8490,11 +8490,11 @@ "is_a": "correlated_with", "domain": "ChemicalEntityOrGeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/biomarker_for", + "multivalued": true, "inherited": true, "owner": "biomarker_for", "inverse": "has_biomarker", "range": "DiseaseOrPhenotypicFeature", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -8522,11 +8522,11 @@ "is_a": "located_in", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/expressed_in", + "multivalued": true, "inherited": true, "owner": "expressed_in", "inverse": "expresses", "range": "AnatomicalEntity", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -8546,11 +8546,11 @@ "is_a": "location_of", "domain": "AnatomicalEntity", "slot_uri": "https://w3id.org/biolink/vocab/expresses", + "multivalued": true, "inherited": true, "owner": "expresses", "inverse": "expressed_in", "range": "GeneOrGeneProduct", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -8591,11 +8591,11 @@ "is_a": "related_to_at_instance_level", "domain": "BiologicalEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_phenotype", + "multivalued": true, "inherited": true, "owner": "has_phenotype", "inverse": "phenotype_of", "range": "PhenotypicFeature", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -8605,11 +8605,11 @@ "is_a": "related_to_at_instance_level", "domain": "PhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/phenotype_of", + "multivalued": true, "inherited": true, "owner": "phenotype_of", "inverse": "has_phenotype", "range": "BiologicalEntity", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -8652,11 +8652,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/occurs_in", + "multivalued": true, "inherited": true, "owner": "occurs_in", "inverse": "contains_process", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -8666,11 +8666,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/contains_process", + "multivalued": true, "inherited": true, "owner": "contains_process", "inverse": "occurs_in", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -8738,11 +8738,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/located_in", + "multivalued": true, "inherited": true, "owner": "located_in", "inverse": "location_of", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -8769,11 +8769,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/location_of", + "multivalued": true, "inherited": true, "owner": "location_of", "inverse": "located_in", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -8788,11 +8788,11 @@ "is_a": "related_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/disease_has_location", + "multivalued": true, "inherited": true, "owner": "disease_has_location", "inverse": "location_of_disease", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -8802,11 +8802,11 @@ "is_a": "related_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/location_of_disease", + "multivalued": true, "inherited": true, "owner": "location_of_disease", "inverse": "disease_has_location", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -8831,11 +8831,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/similar_to", + "multivalued": true, "inherited": true, "owner": "similar_to", "symmetric": true, "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -8865,11 +8865,11 @@ "is_a": "similar_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/chemically_similar_to", + "multivalued": true, "inherited": true, "owner": "chemically_similar_to", "symmetric": true, "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -8890,11 +8890,11 @@ "is_a": "related_to_at_instance_level", "domain": "NucleicAcidEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_sequence_location", + "multivalued": true, "inherited": true, "owner": "has_sequence_location", "inverse": "sequence_location_of", "range": "NucleicAcidEntity", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -8904,11 +8904,11 @@ "is_a": "related_to_at_instance_level", "domain": "NucleicAcidEntity", "slot_uri": "https://w3id.org/biolink/vocab/sequence_location_of", + "multivalued": true, "inherited": true, "owner": "sequence_location_of", "inverse": "has_sequence_location", "range": "NucleicAcidEntity", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -8935,11 +8935,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/model_of", + "multivalued": true, "inherited": true, "owner": "model_of", "inverse": "models", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -8949,11 +8949,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/models", + "multivalued": true, "inherited": true, "owner": "models", "inverse": "model_of", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -8984,11 +8984,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/overlaps", + "multivalued": true, "inherited": true, "owner": "overlaps", "symmetric": true, "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -9053,11 +9053,11 @@ "is_a": "overlaps", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_part", + "multivalued": true, "inherited": true, "owner": "has_part", "inverse": "part_of", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -9081,11 +9081,11 @@ "is_a": "has_part", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_plasma_membrane_part", + "multivalued": true, "inherited": true, "owner": "has_plasma_membrane_part", "inverse": "plasma_membrane_part_of", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -9109,11 +9109,11 @@ "is_a": "related_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/composed_primarily_of", + "multivalued": true, "inherited": true, "owner": "composed_primarily_of", "inverse": "primarily_composed_of", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -9123,11 +9123,11 @@ "is_a": "related_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/primarily_composed_of", + "multivalued": true, "inherited": true, "owner": "primarily_composed_of", "inverse": "composed_primarily_of", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -9137,11 +9137,11 @@ "is_a": "part_of", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/plasma_membrane_part_of", + "multivalued": true, "inherited": true, "owner": "plasma_membrane_part_of", "inverse": "has_plasma_membrane_part", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -9219,11 +9219,11 @@ "is_a": "overlaps", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/part_of", + "multivalued": true, "inherited": true, "owner": "part_of", "inverse": "has_part", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -9268,6 +9268,7 @@ "is_a": "has_participant", "domain": "BiologicalProcessOrActivity", "slot_uri": "https://w3id.org/biolink/vocab/has_input", + "multivalued": true, "inherited": true, "owner": "BiologicalProcessOrActivity", "domain_of": [ @@ -9275,7 +9276,6 @@ ], "inverse": "is_input_of", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -9291,11 +9291,11 @@ "is_a": "participates_in", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/is_input_of", + "multivalued": true, "inherited": true, "owner": "is_input_of", "inverse": "has_input", "range": "BiologicalProcessOrActivity", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -9335,6 +9335,7 @@ "is_a": "has_participant", "domain": "BiologicalProcessOrActivity", "slot_uri": "https://w3id.org/biolink/vocab/has_output", + "multivalued": true, "inherited": true, "owner": "BiologicalProcessOrActivity", "domain_of": [ @@ -9342,7 +9343,6 @@ ], "inverse": "is_output_of", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -9361,11 +9361,11 @@ "is_a": "participates_in", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/is_output_of", + "multivalued": true, "inherited": true, "owner": "is_output_of", "inverse": "has_output", "range": "BiologicalProcessOrActivity", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -9414,11 +9414,11 @@ "is_a": "related_to_at_instance_level", "domain": "BiologicalProcessOrActivity", "slot_uri": "https://w3id.org/biolink/vocab/has_participant", + "multivalued": true, "inherited": true, "owner": "has_participant", "inverse": "participates_in", "range": "Occurrent", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -9439,11 +9439,11 @@ "is_a": "participates_in", "domain": "Occurrent", "slot_uri": "https://w3id.org/biolink/vocab/catalyzes", + "multivalued": true, "inherited": true, "owner": "catalyzes", "inverse": "has_catalyst", "range": "BiologicalProcessOrActivity", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -9453,11 +9453,11 @@ "is_a": "has_participant", "domain": "BiologicalProcessOrActivity", "slot_uri": "https://w3id.org/biolink/vocab/has_catalyst", + "multivalued": true, "inherited": true, "owner": "has_catalyst", "inverse": "catalyzes", "range": "Occurrent", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -9475,11 +9475,11 @@ "is_a": "has_participant", "domain": "ChemicalEntityOrGeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/has_substrate", + "multivalued": true, "inherited": true, "owner": "has_substrate", "inverse": "is_substrate_of", "range": "ChemicalEntityOrGeneOrGeneProduct", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -9490,11 +9490,11 @@ "is_a": "participates_in", "domain": "ChemicalEntityOrGeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/is_substrate_of", + "multivalued": true, "inherited": true, "owner": "is_substrate_of", "inverse": "has_substrate", "range": "ChemicalEntityOrGeneOrGeneProduct", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -9527,11 +9527,11 @@ "is_a": "related_to_at_instance_level", "domain": "Occurrent", "slot_uri": "https://w3id.org/biolink/vocab/participates_in", + "multivalued": true, "inherited": true, "owner": "participates_in", "inverse": "has_participant", "range": "BiologicalProcessOrActivity", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -9565,11 +9565,11 @@ "is_a": "participates_in", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/actively_involved_in", + "multivalued": true, "inherited": true, "owner": "actively_involved_in", "inverse": "actively_involves", "range": "BiologicalProcessOrActivity", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -9582,11 +9582,11 @@ "is_a": "has_participant", "domain": "BiologicalProcessOrActivity", "slot_uri": "https://w3id.org/biolink/vocab/actively_involves", + "multivalued": true, "inherited": true, "owner": "actively_involves", "inverse": "actively_involved_in", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -9614,11 +9614,11 @@ "is_a": "actively_involved_in", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/capable_of", + "multivalued": true, "inherited": true, "owner": "capable_of", "inverse": "can_be_carried_out_by", "range": "Occurrent", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -9629,11 +9629,11 @@ "is_a": "actively_involves", "domain": "Occurrent", "slot_uri": "https://w3id.org/biolink/vocab/can_be_carried_out_by", + "multivalued": true, "inherited": true, "owner": "can_be_carried_out_by", "inverse": "capable_of", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -9657,11 +9657,11 @@ "is_a": "participates_in", "domain": "PhysicalEntity", "slot_uri": "https://w3id.org/biolink/vocab/enables", + "multivalued": true, "inherited": true, "owner": "enables", "inverse": "enabled_by", "range": "BiologicalProcessOrActivity", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -9685,6 +9685,7 @@ "is_a": "has_participant", "domain": "BiologicalProcessOrActivity", "slot_uri": "https://w3id.org/biolink/vocab/enabled_by", + "multivalued": true, "inherited": true, "owner": "BiologicalProcessOrActivity", "domain_of": [ @@ -9692,7 +9693,6 @@ ], "inverse": "enables", "range": "PhysicalEntity", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -9715,11 +9715,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/derives_into", + "multivalued": true, "inherited": true, "owner": "derives_into", "inverse": "derives_from", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -9750,11 +9750,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/derives_from", + "multivalued": true, "inherited": true, "owner": "derives_from", "inverse": "derives_into", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -9774,11 +9774,11 @@ "is_a": "derives_from", "domain": "MolecularEntity", "slot_uri": "https://w3id.org/biolink/vocab/is_metabolite_of", + "multivalued": true, "inherited": true, "owner": "is_metabolite_of", "inverse": "has_metabolite", "range": "MolecularEntity", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -9805,11 +9805,11 @@ "is_a": "derives_into", "domain": "MolecularEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_metabolite", + "multivalued": true, "inherited": true, "owner": "has_metabolite", "inverse": "is_metabolite_of", "range": "MolecularEntity", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -9823,11 +9823,11 @@ "is_a": "part_of", "domain": "ChemicalEntity", "slot_uri": "https://w3id.org/biolink/vocab/food_component_of", + "multivalued": true, "inherited": true, "owner": "food_component_of", "inverse": "has_food_component", "range": "ChemicalEntity", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -9848,11 +9848,11 @@ "is_a": "has_part", "domain": "ChemicalEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_food_component", + "multivalued": true, "inherited": true, "owner": "has_food_component", "inverse": "food_component_of", "range": "ChemicalEntity", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -9866,11 +9866,11 @@ "is_a": "food_component_of", "domain": "ChemicalEntity", "slot_uri": "https://w3id.org/biolink/vocab/nutrient_of", + "multivalued": true, "inherited": true, "owner": "nutrient_of", "inverse": "has_nutrient", "range": "ChemicalEntity", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -9894,11 +9894,11 @@ "is_a": "has_food_component", "domain": "ChemicalEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_nutrient", + "multivalued": true, "inherited": true, "owner": "has_nutrient", "inverse": "nutrient_of", "range": "ChemicalEntity", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -9915,11 +9915,11 @@ "is_a": "part_of", "domain": "MolecularEntity", "slot_uri": "https://w3id.org/biolink/vocab/is_active_ingredient_of", + "multivalued": true, "inherited": true, "owner": "is_active_ingredient_of", "inverse": "has_active_ingredient", "range": "Drug", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -9948,11 +9948,11 @@ "is_a": "has_part", "domain": "Drug", "slot_uri": "https://w3id.org/biolink/vocab/has_active_ingredient", + "multivalued": true, "inherited": true, "owner": "has_active_ingredient", "inverse": "is_active_ingredient_of", "range": "MolecularEntity", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -9969,11 +9969,11 @@ "is_a": "part_of", "domain": "MolecularEntity", "slot_uri": "https://w3id.org/biolink/vocab/is_excipient_of", + "multivalued": true, "inherited": true, "owner": "is_excipient_of", "inverse": "has_excipient", "range": "Drug", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -9997,11 +9997,11 @@ "is_a": "has_part", "domain": "Drug", "slot_uri": "https://w3id.org/biolink/vocab/has_excipient", + "multivalued": true, "inherited": true, "owner": "has_excipient", "inverse": "is_excipient_of", "range": "MolecularEntity", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -10032,11 +10032,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/manifestation_of", + "multivalued": true, "inherited": true, "owner": "manifestation_of", "inverse": "has_manifestation", "range": "Disease", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -10046,11 +10046,11 @@ "is_a": "related_to_at_instance_level", "domain": "Disease", "slot_uri": "https://w3id.org/biolink/vocab/has_manifestation", + "multivalued": true, "inherited": true, "owner": "has_manifestation", "inverse": "manifestation_of", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -10060,11 +10060,11 @@ "is_a": "manifestation_of", "domain": "GeneticInheritance", "slot_uri": "https://w3id.org/biolink/vocab/mode_of_inheritance_of", + "multivalued": true, "inherited": true, "owner": "mode_of_inheritance_of", "inverse": "has_mode_of_inheritance", "range": "DiseaseOrPhenotypicFeature", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -10085,11 +10085,11 @@ "is_a": "has_manifestation", "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/has_mode_of_inheritance", + "multivalued": true, "inherited": true, "owner": "has_mode_of_inheritance", "inverse": "mode_of_inheritance_of", "range": "GeneticInheritance", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -10123,11 +10123,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/produces", + "multivalued": true, "inherited": true, "owner": "produces", "inverse": "produced_by", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -10140,11 +10140,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/produced_by", + "multivalued": true, "inherited": true, "owner": "produced_by", "inverse": "produces", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -10164,11 +10164,11 @@ "is_a": "has_input", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/consumes", + "multivalued": true, "inherited": true, "owner": "consumes", "inverse": "consumed_by", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -10178,11 +10178,11 @@ "is_a": "is_input_of", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/consumed_by", + "multivalued": true, "inherited": true, "owner": "consumed_by", "inverse": "consumes", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -10219,11 +10219,11 @@ "is_a": "related_to_at_instance_level", "domain": "Occurrent", "slot_uri": "https://w3id.org/biolink/vocab/temporally_related_to", + "multivalued": true, "inherited": true, "owner": "temporally_related_to", "symmetric": true, "range": "Occurrent", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10263,11 +10263,11 @@ "is_a": "temporally_related_to", "domain": "Occurrent", "slot_uri": "https://w3id.org/biolink/vocab/precedes", + "multivalued": true, "inherited": true, "owner": "precedes", "inverse": "preceded_by", "range": "Occurrent", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10293,11 +10293,11 @@ "is_a": "temporally_related_to", "domain": "Occurrent", "slot_uri": "https://w3id.org/biolink/vocab/preceded_by", + "multivalued": true, "inherited": true, "owner": "preceded_by", "inverse": "precedes", "range": "Occurrent", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10319,11 +10319,11 @@ "is_a": "has_part", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_variant_part", + "multivalued": true, "inherited": true, "owner": "has_variant_part", "inverse": "variant_part_of", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -10333,11 +10333,11 @@ "is_a": "part_of", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/variant_part_of", + "multivalued": true, "inherited": true, "owner": "variant_part_of", "inverse": "has_variant_part", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -10357,11 +10357,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/related_condition", + "multivalued": true, "inherited": true, "owner": "related_condition", "symmetric": true, "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -10387,11 +10387,11 @@ "is_a": "related_to_at_instance_level", "domain": "SequenceVariant", "slot_uri": "https://w3id.org/biolink/vocab/is_sequence_variant_of", + "multivalued": true, "inherited": true, "owner": "is_sequence_variant_of", "inverse": "has_sequence_variant", "range": "GenomicEntity", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10402,11 +10402,11 @@ "is_a": "related_to_at_instance_level", "domain": "GenomicEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_sequence_variant", + "multivalued": true, "inherited": true, "owner": "has_sequence_variant", "inverse": "is_sequence_variant_of", "range": "SequenceVariant", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -10427,11 +10427,11 @@ "is_a": "is_sequence_variant_of", "domain": "SequenceVariant", "slot_uri": "https://w3id.org/biolink/vocab/is_missense_variant_of", + "multivalued": true, "inherited": true, "owner": "is_missense_variant_of", "inverse": "has_missense_variant", "range": "GenomicEntity", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10442,11 +10442,11 @@ "is_a": "has_sequence_variant", "domain": "GenomicEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_missense_variant", + "multivalued": true, "inherited": true, "owner": "has_missense_variant", "inverse": "is_missense_variant_of", "range": "SequenceVariant", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -10467,11 +10467,11 @@ "is_a": "is_sequence_variant_of", "domain": "SequenceVariant", "slot_uri": "https://w3id.org/biolink/vocab/is_synonymous_variant_of", + "multivalued": true, "inherited": true, "owner": "is_synonymous_variant_of", "inverse": "has_synonymous_variant", "range": "GenomicEntity", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10485,11 +10485,11 @@ "is_a": "has_sequence_variant", "domain": "GenomicEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_synonymous_variant", + "multivalued": true, "inherited": true, "owner": "has_synonymous_variant", "inverse": "is_synonymous_variant_of", "range": "SequenceVariant", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -10510,11 +10510,11 @@ "is_a": "is_sequence_variant_of", "domain": "SequenceVariant", "slot_uri": "https://w3id.org/biolink/vocab/is_nonsense_variant_of", + "multivalued": true, "inherited": true, "owner": "is_nonsense_variant_of", "inverse": "has_nonsense_variant", "range": "GenomicEntity", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10525,11 +10525,11 @@ "is_a": "has_sequence_variant", "domain": "GenomicEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_nonsense_variant", + "multivalued": true, "inherited": true, "owner": "has_nonsense_variant", "inverse": "is_nonsense_variant_of", "range": "SequenceVariant", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -10555,11 +10555,11 @@ "is_a": "is_sequence_variant_of", "domain": "SequenceVariant", "slot_uri": "https://w3id.org/biolink/vocab/is_frameshift_variant_of", + "multivalued": true, "inherited": true, "owner": "is_frameshift_variant_of", "inverse": "has_frameshift_variant", "range": "GenomicEntity", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10575,11 +10575,11 @@ "is_a": "has_sequence_variant", "domain": "GenomicEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_frameshift_variant", + "multivalued": true, "inherited": true, "owner": "has_frameshift_variant", "inverse": "is_frameshift_variant_of", "range": "SequenceVariant", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -10600,11 +10600,11 @@ "is_a": "is_sequence_variant_of", "domain": "SequenceVariant", "slot_uri": "https://w3id.org/biolink/vocab/is_splice_site_variant_of", + "multivalued": true, "inherited": true, "owner": "is_splice_site_variant_of", "inverse": "has_splice_site_variant", "range": "GenomicEntity", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10619,11 +10619,11 @@ "is_a": "has_sequence_variant", "domain": "GenomicEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_splice_site_variant", + "multivalued": true, "inherited": true, "owner": "has_splice_site_variant", "inverse": "is_splice_site_variant_of", "range": "SequenceVariant", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -10641,11 +10641,11 @@ "is_a": "is_sequence_variant_of", "domain": "SequenceVariant", "slot_uri": "https://w3id.org/biolink/vocab/is_nearby_variant_of", + "multivalued": true, "inherited": true, "owner": "is_nearby_variant_of", "inverse": "has_nearby_variant", "range": "GenomicEntity", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10663,11 +10663,11 @@ "is_a": "has_sequence_variant", "domain": "GenomicEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_nearby_variant", + "multivalued": true, "inherited": true, "owner": "has_nearby_variant", "inverse": "is_nearby_variant_of", "range": "SequenceVariant", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -10685,11 +10685,11 @@ "is_a": "is_sequence_variant_of", "domain": "SequenceVariant", "slot_uri": "https://w3id.org/biolink/vocab/is_non_coding_variant_of", + "multivalued": true, "inherited": true, "owner": "is_non_coding_variant_of", "inverse": "has_non_coding_variant", "range": "GenomicEntity", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10700,11 +10700,11 @@ "is_a": "has_sequence_variant", "domain": "GenomicEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_non_coding_variant", + "multivalued": true, "inherited": true, "owner": "has_non_coding_variant", "inverse": "is_non_coding_variant_of", "range": "SequenceVariant", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -10726,11 +10726,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/disease_has_basis_in", + "multivalued": true, "inherited": true, "owner": "disease_has_basis_in", "inverse": "occurs_in_disease", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -10740,11 +10740,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/occurs_in_disease", + "multivalued": true, "inherited": true, "owner": "occurs_in_disease", "inverse": "disease_has_basis_in", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -10765,11 +10765,11 @@ "is_a": "affects", "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/has_adverse_event", + "multivalued": true, "inherited": true, "owner": "has_adverse_event", "inverse": "adverse_event_of", "range": "DiseaseOrPhenotypicFeature", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -10779,11 +10779,11 @@ "is_a": "affected_by", "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/adverse_event_of", + "multivalued": true, "inherited": true, "owner": "adverse_event_of", "inverse": "has_adverse_event", "range": "ChemicalOrDrugOrTreatment", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10811,11 +10811,11 @@ "is_a": "affects", "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/has_side_effect", + "multivalued": true, "inherited": true, "owner": "has_side_effect", "inverse": "is_side_effect_of", "range": "DiseaseOrPhenotypicFeature", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -10825,11 +10825,11 @@ "is_a": "affected_by", "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/is_side_effect_of", + "multivalued": true, "inherited": true, "owner": "is_side_effect_of", "inverse": "has_side_effect", "range": "ChemicalOrDrugOrTreatment", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10859,11 +10859,11 @@ "is_a": "related_to_at_instance_level", "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/contraindicated_in", + "multivalued": true, "inherited": true, "owner": "contraindicated_in", "inverse": "has_contraindication", "range": "BiologicalEntity", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -10883,11 +10883,11 @@ "is_a": "related_to_at_instance_level", "domain": "BiologicalEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_contraindication", + "multivalued": true, "inherited": true, "owner": "has_contraindication", "inverse": "contraindicated_in", "range": "ChemicalOrDrugOrTreatment", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10914,11 +10914,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_not_completed", + "multivalued": true, "inherited": true, "owner": "has_not_completed", "inverse": "not_completed_by", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -10928,11 +10928,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/not_completed_by", + "multivalued": true, "inherited": true, "owner": "not_completed_by", "inverse": "has_not_completed", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -10958,11 +10958,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_completed", + "multivalued": true, "inherited": true, "owner": "has_completed", "inverse": "completed_by", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -10972,11 +10972,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/completed_by", + "multivalued": true, "inherited": true, "owner": "completed_by", "inverse": "has_completed", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -10997,11 +10997,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/in_linkage_disequilibrium_with", + "multivalued": true, "inherited": true, "owner": "in_linkage_disequilibrium_with", "symmetric": true, "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -11026,11 +11026,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_increased_amount", + "multivalued": true, "inherited": true, "owner": "has_increased_amount", "inverse": "increased_amount_of", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -11040,11 +11040,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/increased_amount_of", + "multivalued": true, "inherited": true, "owner": "increased_amount_of", "inverse": "has_increased_amount", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -11069,11 +11069,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_decreased_amount", + "multivalued": true, "inherited": true, "owner": "has_decreased_amount", "inverse": "decreased_amount_in", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -11083,11 +11083,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/decreased_amount_in", + "multivalued": true, "inherited": true, "owner": "decreased_amount_in", "inverse": "has_decreased_amount", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -11116,11 +11116,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/lacks_part", + "multivalued": true, "inherited": true, "owner": "lacks_part", "inverse": "missing_from", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -11130,11 +11130,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/missing_from", + "multivalued": true, "inherited": true, "owner": "missing_from", "inverse": "lacks_part", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -11166,11 +11166,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/develops_from", + "multivalued": true, "inherited": true, "owner": "develops_from", "inverse": "develops_into", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -11180,11 +11180,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/develops_into", + "multivalued": true, "inherited": true, "owner": "develops_into", "inverse": "develops_from", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -11219,6 +11219,7 @@ "is_a": "related_to_at_instance_level", "domain": "ThingWithTaxon", "slot_uri": "https://w3id.org/biolink/vocab/in_taxon", + "multivalued": true, "inherited": true, "owner": "ThingWithTaxon", "domain_of": [ @@ -11226,7 +11227,6 @@ ], "inverse": "taxon_of", "range": "OrganismTaxon", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -11264,11 +11264,11 @@ "is_a": "related_to_at_instance_level", "domain": "OrganismTaxon", "slot_uri": "https://w3id.org/biolink/vocab/taxon_of", + "multivalued": true, "inherited": true, "owner": "taxon_of", "inverse": "in_taxon", "range": "ThingWithTaxon", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -11293,11 +11293,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_molecular_consequence", + "multivalued": true, "inherited": true, "owner": "has_molecular_consequence", "inverse": "is_molecular_consequence_of", "range": "OntologyClass", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -11307,11 +11307,11 @@ "is_a": "related_to_at_instance_level", "domain": "OntologyClass", "slot_uri": "https://w3id.org/biolink/vocab/is_molecular_consequence_of", + "multivalued": true, "inherited": true, "owner": "is_molecular_consequence_of", "inverse": "has_molecular_consequence", "range": "NamedThing", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -11420,12 +11420,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/subject_closure", + "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "string", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -11450,12 +11450,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/object_closure", + "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "string", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -11538,12 +11538,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/subject_category_closure", + "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "OntologyClass", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -11568,12 +11568,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/object_category_closure", + "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "OntologyClass", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -11598,12 +11598,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/subject_label_closure", + "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "string", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -11632,12 +11632,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/object_label_closure", + "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "string", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -11940,12 +11940,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/has_evidence", + "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "EvidenceType", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -12039,12 +12039,12 @@ "is_a": "node_property", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/provided_by", + "multivalued": true, "owner": "NamedThing", "domain_of": [ "NamedThing" ], "range": "string", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -12076,12 +12076,12 @@ "is_a": "knowledge_source", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/aggregator_knowledge_source", + "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "string", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -12095,9 +12095,9 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/supporting_data_source", + "multivalued": true, "owner": "supporting_data_source", "range": "string", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -12108,9 +12108,9 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/supporting_data_set", + "multivalued": true, "owner": "supporting_data_set", "range": "string", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -12342,9 +12342,9 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/supporting_text", + "multivalued": true, "owner": "supporting_text", "range": "string", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -12362,9 +12362,9 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/supporting_documents", + "multivalued": true, "owner": "supporting_documents", "range": "uriorcurie", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -12381,9 +12381,9 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/subject_location_in_text", + "multivalued": true, "owner": "subject_location_in_text", "range": "integer", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -12400,9 +12400,9 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/object_location_in_text", + "multivalued": true, "owner": "object_location_in_text", "range": "integer", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -12592,12 +12592,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/publications", + "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "Publication", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -13030,6 +13030,7 @@ "is_a": "category", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/category", + "multivalued": true, "designates_type": true, "alias": "category", "owner": "NamedThing", @@ -13041,7 +13042,6 @@ "usage_slot_name": "category", "range": "uriorcurie", "required": true, - "multivalued": true, "@type": "SlotDefinition" }, { @@ -13222,6 +13222,7 @@ ], "domain": "Publication", "slot_uri": "http://purl.org/dc/terms/type", + "multivalued": true, "alias": "publication type", "owner": "Publication", "domain_of": [ @@ -13231,7 +13232,6 @@ "usage_slot_name": "publication type", "range": "string", "required": true, - "multivalued": true, "@type": "SlotDefinition" }, { @@ -13245,6 +13245,7 @@ "is_a": "pages", "domain": "Publication", "slot_uri": "https://w3id.org/biolink/vocab/pages", + "multivalued": true, "alias": "pages", "owner": "Publication", "domain_of": [ @@ -13253,7 +13254,6 @@ "is_usage_slot": true, "usage_slot_name": "pages", "range": "string", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -13299,6 +13299,7 @@ "is_a": "type", "domain": "Book", "slot_uri": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "multivalued": true, "alias": "type", "owner": "Book", "domain_of": [ @@ -13307,7 +13308,6 @@ "is_usage_slot": true, "usage_slot_name": "type", "range": "string", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -13380,6 +13380,7 @@ "is_a": "type", "domain": "Serial", "slot_uri": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "multivalued": true, "alias": "type", "owner": "Serial", "domain_of": [ @@ -13388,7 +13389,6 @@ "is_usage_slot": true, "usage_slot_name": "type", "range": "string", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -13545,6 +13545,7 @@ "is_a": "has_input", "domain": "MolecularActivity", "slot_uri": "https://w3id.org/biolink/vocab/has_input", + "multivalued": true, "inherited": true, "alias": "has input", "owner": "MolecularActivity", @@ -13554,7 +13555,6 @@ "is_usage_slot": true, "usage_slot_name": "has input", "range": "MolecularEntity", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -13596,6 +13596,7 @@ "is_a": "has_output", "domain": "MolecularActivity", "slot_uri": "https://w3id.org/biolink/vocab/has_output", + "multivalued": true, "inherited": true, "alias": "has output", "owner": "MolecularActivity", @@ -13605,7 +13606,6 @@ "is_usage_slot": true, "usage_slot_name": "has output", "range": "MolecularEntity", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -13630,6 +13630,7 @@ "is_a": "enabled_by", "domain": "MolecularActivity", "slot_uri": "https://w3id.org/biolink/vocab/enabled_by", + "multivalued": true, "inherited": true, "alias": "enabled by", "owner": "MolecularActivity", @@ -13639,7 +13640,6 @@ "is_usage_slot": true, "usage_slot_name": "enabled by", "range": "MacromolecularMachineMixin", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -13736,6 +13736,7 @@ "is_a": "has_attribute", "domain": "OrganismalEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_attribute", + "multivalued": true, "alias": "has attribute", "owner": "OrganismalEntity", "domain_of": [ @@ -13744,7 +13745,6 @@ "is_usage_slot": true, "usage_slot_name": "has attribute", "range": "Attribute", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -13793,6 +13793,7 @@ "is_a": "has_gene", "domain": "SequenceVariant", "slot_uri": "https://w3id.org/biolink/vocab/has_gene", + "multivalued": true, "alias": "has gene", "owner": "SequenceVariant", "domain_of": [ @@ -13801,7 +13802,6 @@ "is_usage_slot": true, "usage_slot_name": "has gene", "range": "Gene", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -13985,6 +13985,7 @@ "is_a": "has_attribute", "domain": "ClinicalFinding", "slot_uri": "https://w3id.org/biolink/vocab/has_attribute", + "multivalued": true, "alias": "has attribute", "owner": "ClinicalFinding", "domain_of": [ @@ -13993,7 +13994,6 @@ "is_usage_slot": true, "usage_slot_name": "has attribute", "range": "ClinicalAttribute", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -14089,6 +14089,7 @@ "is_a": "has_attribute", "domain": "SocioeconomicExposure", "slot_uri": "https://w3id.org/biolink/vocab/has_attribute", + "multivalued": true, "alias": "has attribute", "owner": "SocioeconomicExposure", "domain_of": [ @@ -14098,7 +14099,6 @@ "usage_slot_name": "has attribute", "range": "SocioeconomicAttribute", "required": true, - "multivalued": true, "@type": "SlotDefinition" }, { @@ -14116,6 +14116,7 @@ "is_a": "type", "domain": "Association", "slot_uri": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "multivalued": true, "alias": "type", "owner": "Association", "domain_of": [ @@ -14124,7 +14125,6 @@ "is_usage_slot": true, "usage_slot_name": "type", "range": "string", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -14138,6 +14138,7 @@ "is_a": "category", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/category", + "multivalued": true, "designates_type": true, "alias": "category", "owner": "Association", @@ -14148,7 +14149,6 @@ "is_usage_slot": true, "usage_slot_name": "category", "range": "uriorcurie", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -14390,6 +14390,7 @@ "is_a": "qualifiers", "domain": "ContributorAssociation", "slot_uri": "https://w3id.org/biolink/vocab/qualifiers", + "multivalued": true, "alias": "qualifiers", "owner": "ContributorAssociation", "domain_of": [ @@ -14398,7 +14399,6 @@ "is_usage_slot": true, "usage_slot_name": "qualifiers", "range": "OntologyClass", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -15747,6 +15747,7 @@ "is_a": "catalyst_qualifier", "domain": "ChemicalToChemicalDerivationAssociation", "slot_uri": "https://w3id.org/biolink/vocab/catalyst_qualifier", + "multivalued": true, "alias": "catalyst qualifier", "owner": "ChemicalToChemicalDerivationAssociation", "domain_of": [ @@ -15755,7 +15756,6 @@ "is_usage_slot": true, "usage_slot_name": "catalyst qualifier", "range": "MacromolecularMachineMixin", - "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -19770,6 +19770,7 @@ "is_a": "has_evidence", "domain": "DruggableGeneToDiseaseAssociation", "slot_uri": "https://w3id.org/biolink/vocab/has_evidence", + "multivalued": true, "alias": "has evidence", "owner": "DruggableGeneToDiseaseAssociation", "domain_of": [ @@ -19778,7 +19779,6 @@ "is_usage_slot": true, "usage_slot_name": "has evidence", "range": "DruggableGeneCategoryEnum", - "multivalued": true, "@type": "SlotDefinition" }, { @@ -35609,9 +35609,9 @@ ], "metamodel_version": "1.7.0", "source_file": "biolink_model.yaml", - "source_file_date": "2024-09-23T16:44:52", + "source_file_date": "2024-09-23T23:51:02", "source_file_size": 400333, - "generation_date": "2024-09-23T16:44:58", + "generation_date": "2024-09-23T23:51:07", "@type": "SchemaDefinition", "@context": [ "project/jsonld/biolink_model.context.jsonld", diff --git a/project/jsonschema/biolink_model.schema.json b/project/jsonschema/biolink_model.schema.json index d98e6bad3..6233ae197 100644 --- a/project/jsonschema/biolink_model.schema.json +++ b/project/jsonschema/biolink_model.schema.json @@ -16,41 +16,26 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": [ - "string", - "null" - ] + "type": "string" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -61,70 +46,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -150,34 +111,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -185,56 +134,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -250,20 +181,14 @@ "properties": { "address": { "description": "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?).", - "type": [ - "string", - "null" - ] + "type": "string" }, "affiliation": { "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.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -277,34 +202,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "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.", @@ -312,56 +225,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -402,34 +297,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -440,70 +323,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -519,10 +378,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -533,10 +389,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -546,44 +399,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -591,10 +429,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -602,24 +437,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "the structure at an earlier time", @@ -627,75 +453,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -703,47 +502,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "description": "the structure at a later time", @@ -751,65 +535,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -829,10 +592,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -843,10 +603,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -856,44 +613,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -901,10 +643,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -912,24 +651,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "the whole", @@ -937,75 +667,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -1013,47 +716,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "description": "the part", @@ -1061,65 +749,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -1164,10 +831,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -1182,47 +846,29 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": [ - "string", - "null" - ] + "type": "string" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "format": { - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "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.", @@ -1230,77 +876,50 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iso_abbreviation": { "description": "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent.", - "type": [ - "string", - "null" - ] + "type": "string" }, "issue": { "description": "issue of a newspaper, a scientific journal or magazine for reference purpose", - "type": [ - "string", - "null" - ] + "type": "string" }, "keywords": { "description": "keywords tagging a publication", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "license": { - "type": [ - "string", - "null" - ] + "type": "string" }, "mesh_terms": { "description": "mesh terms tagging a publication", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "name": { "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).", - "type": [ - "string", - "null" - ] + "type": "string" }, "pages": { "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.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "publication_type": { "description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", @@ -1314,53 +933,35 @@ "type": "string" }, "rights": { - "type": [ - "string", - "null" - ] + "type": "string" }, "summary": { "description": "executive summary of a publication", - "type": [ - "string", - "null" - ] + "type": "string" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "volume": { "description": "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication", - "type": [ - "string", - "null" - ] + "type": "string" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -1378,10 +979,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -1392,10 +990,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -1405,44 +1000,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -1450,10 +1030,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -1461,24 +1038,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "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.", @@ -1486,75 +1054,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -1562,47 +1103,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "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.", @@ -1610,65 +1136,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -1698,34 +1203,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -1733,20 +1226,14 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -1754,56 +1241,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -1830,34 +1299,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -1868,70 +1325,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -1957,64 +1390,43 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "enabled_by": { "description": "holds between a process and a physical entity, where the physical entity executes the process", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_input": { "description": "holds between a process and a continuant, where the continuant is an input into the process", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_output": { "description": "holds between a process and a continuant, where the continuant is an output of the process", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -2025,70 +1437,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -2104,10 +1492,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -2118,10 +1503,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -2131,78 +1513,48 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_count": { "description": "number of things with a particular property", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": [ - "number", - "null" - ] + "type": "number" }, "has_quotient": { - "type": [ - "number", - "null" - ] + "type": "number" }, "has_total": { "description": "total number of things in a particular reference set", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -2210,10 +1562,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -2221,24 +1570,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "behavioral feature that is the object of the association", @@ -2246,37 +1586,25 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -2287,45 +1615,27 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -2333,61 +1643,40 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualified_predicate": { "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 \u2018full statement\u2019 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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject": { "description": "behavior that is the subject of the association", @@ -2395,37 +1684,25 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -2436,35 +1713,23 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -2494,34 +1759,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -2529,20 +1782,14 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -2550,64 +1797,43 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -2634,34 +1860,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -2672,70 +1886,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -2767,64 +1957,43 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "enabled_by": { "description": "holds between a process and a physical entity, where the physical entity executes the process", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_input": { "description": "holds between a process and a continuant, where the continuant is an input into the process", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_output": { "description": "holds between a process and a continuant, where the continuant is an output of the process", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -2835,70 +2004,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -2924,64 +2069,43 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "enabled_by": { "description": "holds between a process and a physical entity, where the physical entity executes the process", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_input": { "description": "holds between a process and a continuant, where the continuant is an input into the process", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_output": { "description": "holds between a process and a continuant, where the continuant is an output of the process", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -2992,70 +2116,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -3081,34 +2181,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -3116,20 +2204,14 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -3137,56 +2219,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -3213,34 +2277,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -3248,20 +2300,14 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -3269,64 +2315,43 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -3346,10 +2371,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -3364,47 +2386,29 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": [ - "string", - "null" - ] + "type": "string" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "format": { - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "Books should have industry-standard identifier such as from ISBN.", @@ -3412,63 +2416,42 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "keywords": { "description": "keywords tagging a publication", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "license": { - "type": [ - "string", - "null" - ] + "type": "string" }, "mesh_terms": { "description": "mesh terms tagging a publication", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "name": { "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).", - "type": [ - "string", - "null" - ] + "type": "string" }, "pages": { "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.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "publication_type": { "description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", @@ -3478,47 +2461,32 @@ "type": "array" }, "rights": { - "type": [ - "string", - "null" - ] + "type": "string" }, "summary": { "description": "executive summary of a publication", - "type": [ - "string", - "null" - ] + "type": "string" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "description": "Should generally be set to an ontology class defined term for 'book'.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -3538,10 +2506,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -3555,55 +2520,34 @@ }, "chapter": { "description": "chapter of a book", - "type": [ - "string", - "null" - ] + "type": "string" }, "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": [ - "string", - "null" - ] + "type": "string" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "format": { - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "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.", @@ -3611,63 +2555,42 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "keywords": { "description": "keywords tagging a publication", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "license": { - "type": [ - "string", - "null" - ] + "type": "string" }, "mesh_terms": { "description": "mesh terms tagging a publication", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "name": { "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).", - "type": [ - "string", - "null" - ] + "type": "string" }, "pages": { "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.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "publication_type": { "description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", @@ -3681,53 +2604,35 @@ "type": "string" }, "rights": { - "type": [ - "string", - "null" - ] + "type": "string" }, "summary": { "description": "executive summary of a publication", - "type": [ - "string", - "null" - ] + "type": "string" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "volume": { "description": "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication", - "type": [ - "string", - "null" - ] + "type": "string" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -3755,34 +2660,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -3793,70 +2686,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -3872,10 +2741,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -3886,10 +2752,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -3899,78 +2762,48 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_count": { "description": "number of things with a particular property", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": [ - "number", - "null" - ] + "type": "number" }, "has_quotient": { - "type": [ - "number", - "null" - ] + "type": "number" }, "has_total": { "description": "total number of things in a particular reference set", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -3978,10 +2811,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -3989,24 +2819,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "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.", @@ -4014,37 +2835,25 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -4055,45 +2864,27 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -4101,61 +2892,40 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualified_predicate": { "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 \u2018full statement\u2019 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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject": { "description": "the case (e.g. patient) that has the property", @@ -4163,37 +2933,25 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -4204,35 +2962,23 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -4252,10 +2998,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -4266,10 +3009,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -4279,78 +3019,48 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_count": { "description": "number of things with a particular property", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": [ - "number", - "null" - ] + "type": "number" }, "has_quotient": { - "type": [ - "number", - "null" - ] + "type": "number" }, "has_total": { "description": "total number of things in a particular reference set", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -4358,10 +3068,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -4369,24 +3076,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "disease", @@ -4394,37 +3092,25 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -4435,45 +3121,27 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -4481,61 +3149,40 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualified_predicate": { "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 \u2018full statement\u2019 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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -4547,30 +3194,21 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -4581,35 +3219,23 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -4664,34 +3290,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -4702,70 +3316,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -4791,34 +3381,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -4829,70 +3407,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -4908,10 +3462,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -4922,10 +3473,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -4935,51 +3483,33 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -4987,10 +3517,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -4998,24 +3525,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "disease", @@ -5023,37 +3541,25 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -5064,45 +3570,27 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "The relationship to the disease", @@ -5110,54 +3598,36 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualified_predicate": { "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 \u2018full statement\u2019 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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "description": "A cell line derived from an organismal entity with a disease state that is used as a model of that disease.", @@ -5165,37 +3635,25 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -5206,35 +3664,23 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -5254,10 +3700,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -5268,10 +3711,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -5281,44 +3721,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -5326,10 +3751,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -5337,24 +3759,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "disease or phenotype", @@ -5362,75 +3775,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -5438,47 +3824,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "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.", @@ -5486,65 +3857,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -5574,34 +3924,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -5612,70 +3950,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -5701,34 +4015,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -5739,70 +4041,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -5818,10 +4096,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -5832,17 +4107,11 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "anatomical_context_qualifier": { "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).", - "type": [ - "string", - "null" - ] + "type": "string" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -5852,10 +4121,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "causal_mechanism_qualifier": { "$ref": "#/$defs/CausalMechanismQualifierEnum", @@ -5863,37 +4129,25 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -5901,10 +4155,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -5912,24 +4163,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -5941,36 +4183,24 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_context_qualifier": { - "type": [ - "string", - "null" - ] + "type": "string" }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -5985,17 +4215,11 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_part_qualifier": { "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum", @@ -6003,31 +4227,19 @@ }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -6035,61 +4247,40 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualified_predicate": { "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 \u2018full statement\u2019 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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "species_context_qualifier": { "description": "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject": { "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.", @@ -6101,36 +4292,24 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_context_qualifier": { - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_derivative_qualifier": { "$ref": "#/$defs/ChemicalEntityDerivativeEnum", @@ -6149,17 +4328,11 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_part_qualifier": { "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum", @@ -6168,20 +4341,14 @@ "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -6204,10 +4371,7 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -6221,44 +4385,29 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -6266,77 +4415,50 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "is_toxic": { "description": "", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "max_tolerated_dose": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "trade_name": { "description": "", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -6352,10 +4474,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -6366,10 +4485,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -6379,44 +4495,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -6424,10 +4525,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -6435,24 +4533,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "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.", @@ -6460,75 +4549,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -6536,47 +4598,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "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.", @@ -6584,65 +4631,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -6670,10 +4696,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -6684,10 +4707,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -6697,44 +4717,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -6742,10 +4747,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -6753,24 +4755,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -6778,30 +4771,21 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -6812,45 +4796,27 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "the direction is always from regulator to regulated", @@ -6858,47 +4824,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", @@ -6906,65 +4857,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -6994,34 +4924,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -7029,20 +4947,14 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -7050,64 +4962,43 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -7124,10 +5015,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -7138,17 +5026,11 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "anatomical_context_qualifier": { "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).", - "type": [ - "string", - "null" - ] + "type": "string" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -7158,44 +5040,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -7203,10 +5070,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -7214,24 +5078,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -7239,36 +5094,24 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_context_qualifier": { - "type": [ - "string", - "null" - ] + "type": "string" }, "object_form_or_variant_qualifier": { "$ref": "#/$defs/ChemicalOrGeneOrGeneProductFormOrVariantEnum", @@ -7279,17 +5122,11 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_part_qualifier": { "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum", @@ -7297,31 +5134,19 @@ }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -7329,47 +5154,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "description": "the chemical entity or entity that is an interactor", @@ -7377,36 +5187,24 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_context_qualifier": { - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_derivative_qualifier": { "$ref": "#/$defs/ChemicalEntityDerivativeEnum", @@ -7421,17 +5219,11 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_part_qualifier": { "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum", @@ -7440,20 +5232,14 @@ "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -7476,10 +5262,7 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -7493,17 +5276,11 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "drug_regulatory_status_world_wide": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -7511,30 +5288,21 @@ }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "highest_FDA_approval_status": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -7546,94 +5314,61 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "is_supplement": { "description": "", - "type": [ - "string", - "null" - ] + "type": "string" }, "is_toxic": { "description": "", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "max_tolerated_dose": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "routes_of_delivery": { "description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": { "$ref": "#/$defs/DrugDeliveryEnum" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "trade_name": { "description": "", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -7653,10 +5388,7 @@ }, "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -7667,10 +5399,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -7680,44 +5409,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -7725,10 +5439,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -7736,24 +5447,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "disease or phenotype", @@ -7761,75 +5463,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -7837,47 +5512,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", @@ -7885,65 +5545,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -7967,10 +5606,7 @@ }, "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -7981,10 +5617,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -7994,44 +5627,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -8039,10 +5657,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -8050,24 +5665,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "disease or phenotype", @@ -8075,75 +5681,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -8151,47 +5730,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", @@ -8199,65 +5763,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -8301,34 +5844,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -8336,20 +5867,14 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -8357,56 +5882,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -8423,10 +5930,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -8437,10 +5941,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -8450,44 +5951,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -8495,10 +5981,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -8506,24 +5989,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "the chemical element that is the target of the statement", @@ -8531,75 +6005,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -8607,47 +6054,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", @@ -8655,65 +6087,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -8733,10 +6144,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -8747,20 +6155,14 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "catalyst_qualifier": { "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.", "items": { "$ref": "#/$defs/MacromolecularMachineMixin" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -8770,44 +6172,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -8815,10 +6202,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -8826,24 +6210,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "the downstream chemical entity", @@ -8851,75 +6226,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -8927,47 +6275,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "description": "the upstream chemical entity", @@ -8975,65 +6308,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -9053,10 +6365,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -9067,10 +6376,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -9080,44 +6386,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -9125,10 +6416,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -9136,24 +6424,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "the disease or phenotype that is affected by the chemical", @@ -9161,75 +6440,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -9237,47 +6489,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", @@ -9285,65 +6522,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -9363,10 +6579,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -9377,10 +6590,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -9390,44 +6600,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -9435,10 +6630,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -9446,24 +6638,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "the pathway that is affected by the chemical", @@ -9471,75 +6654,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -9547,47 +6703,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "description": "the chemical entity that is affecting the pathway", @@ -9595,65 +6736,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -9684,47 +6804,29 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": [ - "string", - "null" - ] + "type": "string" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "format": { - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -9732,68 +6834,44 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "license": { - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "rights": { - "type": [ - "string", - "null" - ] + "type": "string" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -9832,34 +6910,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -9867,20 +6933,14 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -9888,56 +6948,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -9964,34 +7006,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -9999,20 +7029,14 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -10020,56 +7044,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -10096,34 +7102,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -10131,56 +7125,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -10206,34 +7182,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -10244,70 +7208,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -10333,34 +7273,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -10368,56 +7296,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -10443,34 +7353,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -10478,20 +7376,14 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -10499,56 +7391,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -10575,34 +7449,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -10610,20 +7472,14 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -10631,56 +7487,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -10707,34 +7545,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -10742,56 +7568,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -10817,41 +7625,26 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": [ - "string", - "null" - ] + "type": "string" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -10862,70 +7655,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -10951,34 +7720,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -10989,70 +7746,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -11079,47 +7812,29 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": [ - "string", - "null" - ] + "type": "string" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "format": { - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -11127,68 +7842,44 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "license": { - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "rights": { - "type": [ - "string", - "null" - ] + "type": "string" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -11214,34 +7905,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -11249,20 +7928,14 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -11270,56 +7943,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -11339,10 +7994,7 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -11356,17 +8008,11 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "drug_regulatory_status_world_wide": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -11374,30 +8020,21 @@ }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "highest_FDA_approval_status": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -11409,94 +8046,61 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "is_supplement": { "description": "", - "type": [ - "string", - "null" - ] + "type": "string" }, "is_toxic": { "description": "", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "max_tolerated_dose": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "routes_of_delivery": { "description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": { "$ref": "#/$defs/DrugDeliveryEnum" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "trade_name": { "description": "", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -11523,47 +8127,29 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": [ - "string", - "null" - ] + "type": "string" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "format": { - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -11571,68 +8157,44 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "license": { - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "rights": { - "type": [ - "string", - "null" - ] + "type": "string" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -11659,47 +8221,29 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": [ - "string", - "null" - ] + "type": "string" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "format": { - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -11707,68 +8251,44 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "license": { - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "rights": { - "type": [ - "string", - "null" - ] + "type": "string" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -11784,10 +8304,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -11798,10 +8315,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -11811,44 +8325,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -11856,10 +8355,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -11867,24 +8363,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "agent helping to realise the given entity (e.g. such as a publication)", @@ -11892,75 +8379,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'", @@ -11968,47 +8428,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "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'", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "description": "information content entity which an agent has helped realise", @@ -12016,65 +8461,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -12094,10 +8518,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -12108,10 +8529,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -12121,78 +8539,48 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_count": { "description": "number of things with a particular property", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": [ - "number", - "null" - ] + "type": "number" }, "has_quotient": { - "type": [ - "number", - "null" - ] + "type": "number" }, "has_total": { "description": "total number of things in a particular reference set", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -12200,10 +8588,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -12211,24 +8596,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "disease", @@ -12236,37 +8612,25 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -12277,45 +8641,27 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -12323,61 +8669,40 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualified_predicate": { "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 \u2018full statement\u2019 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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -12389,30 +8714,21 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -12423,35 +8739,23 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -12482,47 +8786,29 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": [ - "string", - "null" - ] + "type": "string" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "format": { - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -12530,68 +8816,44 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "license": { - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "rights": { - "type": [ - "string", - "null" - ] + "type": "string" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -12618,53 +8880,32 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": [ - "string", - "null" - ] + "type": "string" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "distribution_download_url": { - "type": [ - "string", - "null" - ] + "type": "string" }, "format": { - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -12672,68 +8913,44 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "license": { - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "rights": { - "type": [ - "string", - "null" - ] + "type": "string" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -12760,47 +8977,29 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": [ - "string", - "null" - ] + "type": "string" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "format": { - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -12808,80 +9007,50 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "license": { - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "rights": { - "type": [ - "string", - "null" - ] + "type": "string" }, "source_logo": { - "type": [ - "string", - "null" - ] + "type": "string" }, "source_web_page": { - "type": [ - "string", - "null" - ] + "type": "string" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -12908,134 +9077,83 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": [ - "string", - "null" - ] + "type": "string" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "format": { - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_dataset": { - "type": [ - "string", - "null" - ] + "type": "string" }, "has_distribution": { - "type": [ - "string", - "null" - ] + "type": "string" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, "ingest_date": { - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "license": { - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "rights": { - "type": [ - "string", - "null" - ] + "type": "string" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -13061,34 +9179,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -13096,56 +9202,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -13171,34 +9259,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -13206,56 +9282,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -13292,34 +9350,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -13330,70 +9376,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -13419,34 +9441,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -13457,70 +9467,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -13546,34 +9532,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -13581,20 +9555,14 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -13602,64 +9570,43 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -13682,10 +9629,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -13696,10 +9640,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -13709,44 +9650,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -13754,10 +9680,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -13765,24 +9688,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "genetic inheritance associated with the specified disease or phenotypic feature.", @@ -13790,75 +9704,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -13866,47 +9753,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "description": "disease or phenotype", @@ -13914,65 +9786,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -13992,10 +9843,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -14006,10 +9854,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -14019,44 +9864,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -14064,10 +9894,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -14075,24 +9902,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "anatomical entity in which the disease or feature is found.", @@ -14100,75 +9918,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -14176,47 +9967,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "description": "disease or phenotype", @@ -14224,65 +10000,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -14302,10 +10057,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -14316,10 +10068,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -14329,44 +10078,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -14374,10 +10108,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -14385,24 +10116,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "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.", @@ -14410,75 +10132,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -14486,47 +10181,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "description": "disease class", @@ -14534,65 +10214,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -14612,10 +10271,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -14626,10 +10282,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -14639,78 +10292,48 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_count": { "description": "number of things with a particular property", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": [ - "number", - "null" - ] + "type": "number" }, "has_quotient": { - "type": [ - "number", - "null" - ] + "type": "number" }, "has_total": { "description": "total number of things in a particular reference set", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -14718,10 +10341,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -14729,24 +10349,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "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.", @@ -14754,37 +10365,25 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -14795,52 +10394,31 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "onset_qualifier": { "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -14848,61 +10426,40 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualified_predicate": { "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 \u2018full statement\u2019 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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject": { "description": "disease class", @@ -14910,37 +10467,25 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -14951,35 +10496,23 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -15002,10 +10535,7 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -15019,17 +10549,11 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "drug_regulatory_status_world_wide": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -15037,30 +10561,21 @@ }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "highest_FDA_approval_status": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -15072,94 +10587,61 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "is_supplement": { "description": "", - "type": [ - "string", - "null" - ] + "type": "string" }, "is_toxic": { "description": "", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "max_tolerated_dose": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "routes_of_delivery": { "description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": { "$ref": "#/$defs/DrugDeliveryEnum" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "trade_name": { "description": "", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -15205,34 +10687,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -15240,20 +10710,14 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -15261,64 +10725,43 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -15338,10 +10781,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -15356,47 +10796,29 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": [ - "string", - "null" - ] + "type": "string" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "format": { - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "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.", @@ -15404,63 +10826,42 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "keywords": { "description": "keywords tagging a publication", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "license": { - "type": [ - "string", - "null" - ] + "type": "string" }, "mesh_terms": { "description": "mesh terms tagging a publication", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "name": { "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).", - "type": [ - "string", - "null" - ] + "type": "string" }, "pages": { "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.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "publication_type": { "description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", @@ -15470,46 +10871,31 @@ "type": "array" }, "rights": { - "type": [ - "string", - "null" - ] + "type": "string" }, "summary": { "description": "executive summary of a publication", - "type": [ - "string", - "null" - ] + "type": "string" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -15526,10 +10912,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -15540,10 +10923,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -15553,44 +10933,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -15598,10 +10963,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -15609,24 +10971,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -15634,75 +10987,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -15710,47 +11036,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "description": "the drug that is an interactor", @@ -15758,65 +11069,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -15846,34 +11136,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -15884,27 +11162,18 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -15912,64 +11181,43 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -15997,10 +11245,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -16011,10 +11256,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -16024,78 +11266,48 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_count": { "description": "number of things with a particular property", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "$ref": "#/$defs/DruggableGeneCategoryEnum" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": [ - "number", - "null" - ] + "type": "number" }, "has_quotient": { - "type": [ - "number", - "null" - ] + "type": "number" }, "has_total": { "description": "total number of things in a particular reference set", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -16103,10 +11315,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -16114,24 +11323,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "disease", @@ -16139,37 +11339,25 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -16180,45 +11368,27 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -16226,61 +11396,40 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualified_predicate": { "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 \u2018full statement\u2019 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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -16292,30 +11441,21 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -16326,35 +11466,23 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -16374,10 +11502,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -16388,10 +11513,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -16401,10 +11523,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "clinical_approval_status": { "$ref": "#/$defs/ClinicalApprovalStatusEnum", @@ -16412,37 +11531,25 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -16450,10 +11557,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -16461,27 +11565,18 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "max_research_phase": { "$ref": "#/$defs/MaxResearchPhaseEnum" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "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.", @@ -16489,75 +11584,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -16565,47 +11633,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "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.", @@ -16613,65 +11666,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -16691,10 +11723,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -16705,10 +11734,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -16718,10 +11744,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "clinical_approval_status": { "$ref": "#/$defs/ClinicalApprovalStatusEnum", @@ -16729,37 +11752,25 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -16767,10 +11778,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -16778,27 +11786,18 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "max_research_phase": { "$ref": "#/$defs/MaxResearchPhaseEnum" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "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.", @@ -16806,75 +11805,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -16882,47 +11854,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "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.", @@ -16930,65 +11887,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -17018,34 +11954,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -17053,20 +11977,14 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -17074,64 +11992,43 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -17158,34 +12055,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -17193,56 +12078,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -17261,10 +12128,7 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -17278,44 +12142,29 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -17323,77 +12172,50 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "is_toxic": { "description": "", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "max_tolerated_dose": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "trade_name": { "description": "", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -17419,34 +12241,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -17454,56 +12264,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -17535,34 +12327,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -17570,56 +12350,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -17646,47 +12408,29 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": [ - "string", - "null" - ] + "type": "string" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "format": { - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -17694,68 +12438,44 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "license": { - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "rights": { - "type": [ - "string", - "null" - ] + "type": "string" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -17781,34 +12501,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -17819,70 +12527,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -17898,10 +12582,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -17912,10 +12593,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -17925,44 +12603,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -17970,10 +12633,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -17981,24 +12641,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "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.", @@ -18006,75 +12657,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -18082,47 +12706,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "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.", @@ -18130,65 +12739,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -18208,10 +12796,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -18222,10 +12807,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -18235,44 +12817,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -18280,10 +12847,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -18291,24 +12855,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "$ref": "#/$defs/Outcome", @@ -18316,82 +12871,52 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "population_context_qualifier": { "description": "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association.", - "type": [ - "string", - "null" - ] + "type": "string" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -18399,47 +12924,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "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.", @@ -18447,73 +12957,49 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "temporal_context_qualifier": { "description": "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier.", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -18533,10 +13019,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -18547,10 +13030,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -18560,78 +13040,48 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_count": { "description": "number of things with a particular property", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": [ - "number", - "null" - ] + "type": "number" }, "has_quotient": { - "type": [ - "number", - "null" - ] + "type": "number" }, "has_total": { "description": "total number of things in a particular reference set", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -18639,10 +13089,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -18650,24 +13097,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "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.", @@ -18675,37 +13113,25 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -18716,45 +13142,27 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -18762,61 +13170,40 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualified_predicate": { "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 \u2018full statement\u2019 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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject": { "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.", @@ -18824,37 +13211,25 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -18865,35 +13240,23 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -18927,10 +13290,7 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -18944,17 +13304,11 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "drug_regulatory_status_world_wide": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -18962,30 +13316,21 @@ }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "highest_FDA_approval_status": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -18997,94 +13342,61 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "is_supplement": { "description": "", - "type": [ - "string", - "null" - ] + "type": "string" }, "is_toxic": { "description": "", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "max_tolerated_dose": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "routes_of_delivery": { "description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": { "$ref": "#/$defs/DrugDeliveryEnum" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "trade_name": { "description": "", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -19103,10 +13415,7 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -19120,44 +13429,29 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -19165,77 +13459,50 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "is_toxic": { "description": "", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "max_tolerated_dose": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "trade_name": { "description": "", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -19251,10 +13518,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -19265,10 +13529,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -19278,44 +13539,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -19323,10 +13569,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -19334,24 +13577,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "class describing the activity, process or localization of the gene product", @@ -19359,75 +13593,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -19435,47 +13642,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "$ref": "#/$defs/MacromolecularMachineMixin", @@ -19483,65 +13675,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -19571,34 +13742,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -19609,70 +13768,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -19698,41 +13833,26 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": [ - "string", - "null" - ] + "type": "string" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -19743,77 +13863,50 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "symbol": { "description": "Symbol for a particular thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -19829,10 +13922,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -19843,17 +13933,11 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "anatomical_context_qualifier": { "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).", - "type": [ - "string", - "null" - ] + "type": "string" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -19863,10 +13947,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "causal_mechanism_qualifier": { "$ref": "#/$defs/CausalMechanismQualifierEnum", @@ -19874,37 +13955,25 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -19912,10 +13981,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -19923,24 +13989,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "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.", @@ -19952,36 +14009,24 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_context_qualifier": { - "type": [ - "string", - "null" - ] + "type": "string" }, "object_derivative_qualifier": { "$ref": "#/$defs/ChemicalEntityDerivativeEnum", @@ -20000,17 +14045,11 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_part_qualifier": { "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum", @@ -20018,31 +14057,19 @@ }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -20050,61 +14077,40 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualified_predicate": { "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 \u2018full statement\u2019 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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "species_context_qualifier": { "description": "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -20116,43 +14122,28 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_context_qualifier": { - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_derivative_qualifier": { "description": "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier \u2018metabolite\u2019 combines with a \u2018Chemical X\u2019 core concept to express the composed concept \u2018a metabolite of Chemical X\u2019. This qualifier is for the subject of an association (or statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -20167,17 +14158,11 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_part_qualifier": { "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum", @@ -20186,20 +14171,14 @@ "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -20219,10 +14198,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -20233,10 +14209,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -20246,78 +14219,48 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_count": { "description": "number of things with a particular property", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": [ - "number", - "null" - ] + "type": "number" }, "has_quotient": { - "type": [ - "number", - "null" - ] + "type": "number" }, "has_total": { "description": "total number of things in a particular reference set", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -20325,10 +14268,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -20336,24 +14276,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "disease", @@ -20361,37 +14292,25 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -20402,45 +14321,27 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "The relationship to the disease", @@ -20448,61 +14349,40 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualified_predicate": { "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 \u2018full statement\u2019 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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -20514,30 +14394,21 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -20548,35 +14419,23 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -20606,44 +14465,29 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_gene_or_gene_product": { "description": "connects an entity with one or more gene or gene products", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -20654,70 +14498,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -20733,10 +14553,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -20747,10 +14564,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -20760,78 +14574,48 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_count": { "description": "number of things with a particular property", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": [ - "number", - "null" - ] + "type": "number" }, "has_quotient": { - "type": [ - "number", - "null" - ] + "type": "number" }, "has_total": { "description": "total number of things in a particular reference set", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -20839,10 +14623,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -20850,24 +14631,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "disease", @@ -20875,37 +14647,25 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -20916,45 +14676,27 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -20962,61 +14704,40 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualified_predicate": { "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 \u2018full statement\u2019 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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -21028,30 +14749,21 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -21059,45 +14771,30 @@ }, "subject_form_or_variant_qualifier": { "description": "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier \u2018mutation\u2019 combines with the core concept \u2018Gene X\u2019 to express the compose concept \u2018a mutation of Gene X\u2019. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -21192,10 +14889,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -21206,10 +14900,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -21219,44 +14910,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -21264,10 +14940,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -21275,24 +14948,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -21304,30 +14968,21 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -21338,45 +14993,27 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -21384,20 +15021,14 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualified_predicate": { "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 \u2018full statement\u2019 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.", @@ -21405,37 +15036,25 @@ }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "species_context_qualifier": { "description": "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -21443,65 +15062,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -21524,10 +15122,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -21538,10 +15133,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -21551,78 +15143,48 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_count": { "description": "number of things with a particular property", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": [ - "number", - "null" - ] + "type": "number" }, "has_quotient": { - "type": [ - "number", - "null" - ] + "type": "number" }, "has_total": { "description": "total number of things in a particular reference set", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -21630,10 +15192,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -21641,24 +15200,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "disease", @@ -21666,37 +15216,25 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -21707,45 +15245,27 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -21753,61 +15273,40 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualified_predicate": { "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 \u2018full statement\u2019 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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -21819,30 +15318,21 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -21853,35 +15343,23 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -21901,10 +15379,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -21915,10 +15390,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -21928,78 +15400,48 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_count": { "description": "number of things with a particular property", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": [ - "number", - "null" - ] + "type": "number" }, "has_quotient": { - "type": [ - "number", - "null" - ] + "type": "number" }, "has_total": { "description": "total number of things in a particular reference set", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -22007,10 +15449,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -22018,24 +15457,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "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.", @@ -22043,37 +15473,25 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -22084,45 +15502,27 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -22130,61 +15530,40 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualified_predicate": { "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 \u2018full statement\u2019 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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -22196,30 +15575,21 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -22230,35 +15600,23 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -22278,10 +15636,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -22292,10 +15647,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -22305,44 +15657,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -22350,10 +15687,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -22361,24 +15695,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "location in which the gene is expressed", @@ -22386,75 +15711,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "expression relationship", @@ -22462,61 +15760,40 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "quantifier_qualifier": { "description": "can be used to indicate magnitude, or also ranking", - "type": [ - "string", - "null" - ] + "type": "string" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "stage_qualifier": { "description": "stage at which the gene is expressed in the site", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -22524,65 +15801,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -22602,10 +15858,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -22616,10 +15869,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -22629,51 +15879,33 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "expression_site": { "description": "location in which gene or protein expression takes place. May be cell, tissue, or organ.", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -22681,10 +15913,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -22692,24 +15921,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -22717,82 +15937,52 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "phenotypic_state": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -22800,61 +15990,40 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "quantifier_qualifier": { "description": "Optional quantitative value indicating degree of expression.", - "type": [ - "string", - "null" - ] + "type": "string" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "stage_qualifier": { "description": "stage during which gene or protein expression of takes place.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -22862,65 +16031,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -22940,10 +16088,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -22954,10 +16099,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -22967,44 +16109,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -23012,10 +16139,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -23023,24 +16147,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "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.", @@ -23048,75 +16163,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "membership of the gene in the given gene family.", @@ -23124,47 +16212,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "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.", @@ -23172,65 +16245,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -23250,10 +16302,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -23264,10 +16313,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -23277,44 +16323,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -23322,10 +16353,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -23333,24 +16361,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -23358,75 +16377,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "homology relationship type", @@ -23434,47 +16426,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -23482,65 +16459,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -23560,10 +16516,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -23574,10 +16527,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -23587,44 +16537,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -23632,10 +16567,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -23643,24 +16575,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "$ref": "#/$defs/GeneProductMixin", @@ -23668,75 +16591,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -23744,47 +16640,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "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.", @@ -23792,65 +16673,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -23870,10 +16730,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -23884,10 +16741,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -23897,44 +16751,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -23942,10 +16781,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -23953,24 +16789,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "class describing the activity, process or localization of the gene product", @@ -23978,75 +16805,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -24054,47 +16854,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "description": "gene, product or macromolecular complex that has the function associated with the GO term", @@ -24102,65 +16887,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -24180,10 +16944,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -24194,10 +16955,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -24207,44 +16965,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -24252,10 +16995,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -24263,24 +17003,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "the pathway that includes or is affected by the gene or gene product", @@ -24288,75 +17019,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -24364,47 +17068,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -24412,65 +17101,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -24490,10 +17158,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -24504,10 +17169,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -24517,78 +17179,48 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_count": { "description": "number of things with a particular property", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": [ - "number", - "null" - ] + "type": "number" }, "has_quotient": { - "type": [ - "number", - "null" - ] + "type": "number" }, "has_total": { "description": "total number of things in a particular reference set", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -24596,10 +17228,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -24607,24 +17236,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "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.", @@ -24632,37 +17252,25 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -24673,45 +17281,27 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -24719,61 +17309,40 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualified_predicate": { "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 \u2018full statement\u2019 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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -24785,30 +17354,21 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -24819,35 +17379,23 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -24877,34 +17425,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -24915,70 +17451,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -25004,41 +17516,26 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": [ - "string", - "null" - ] + "type": "string" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -25049,70 +17546,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -25138,34 +17611,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -25173,37 +17634,25 @@ }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_gene_or_gene_product": { "description": "connects an entity with one or more gene or gene products", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -25214,78 +17663,51 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -25302,10 +17724,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -25316,10 +17735,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -25329,31 +17745,19 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "end_interbase_coordinate": { "description": "The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on.", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "genome_build": { "$ref": "#/$defs/StrandEnum", @@ -25364,20 +17768,14 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -25385,10 +17783,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -25396,24 +17791,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "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.", @@ -25421,75 +17807,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "phase": { "$ref": "#/$defs/PhaseEnum", @@ -25501,54 +17860,36 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "start_interbase_coordinate": { "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).", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "strand": { "$ref": "#/$defs/StrandEnum", @@ -25560,65 +17901,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -25648,47 +17968,29 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_zygosity": { - "type": [ - "string", - "null" - ] + "type": "string" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -25699,70 +18001,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -25778,10 +18056,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -25792,10 +18067,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -25805,51 +18077,33 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -25857,10 +18111,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -25868,24 +18119,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "disease", @@ -25893,37 +18135,25 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -25934,45 +18164,27 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "The relationship to the disease", @@ -25980,54 +18192,36 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualified_predicate": { "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 \u2018full statement\u2019 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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "description": "A genotype that has a role in modeling the disease.", @@ -26035,37 +18229,25 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -26076,35 +18258,23 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -26124,10 +18294,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -26138,10 +18305,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -26151,51 +18315,33 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -26203,10 +18349,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -26214,24 +18357,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "a disease that is associated with that genotype", @@ -26239,37 +18373,25 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -26280,45 +18402,27 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "E.g. is pathogenic for", @@ -26326,54 +18430,36 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualified_predicate": { "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 \u2018full statement\u2019 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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "description": "a genotype that is associated in some way with a disease state", @@ -26381,37 +18467,25 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -26422,35 +18496,23 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -26470,10 +18532,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -26484,10 +18543,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -26497,44 +18553,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -26542,10 +18583,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -26553,24 +18591,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "gene implicated in genotype", @@ -26578,75 +18607,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "the relationship type used to connect genotype to gene", @@ -26654,47 +18656,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "description": "parent genotype", @@ -26702,65 +18689,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -26780,10 +18746,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -26794,10 +18757,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -26807,44 +18767,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -26852,10 +18797,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -26863,24 +18805,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "child genotype", @@ -26888,75 +18821,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -26964,47 +18870,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "description": "parent genotype", @@ -27012,65 +18903,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -27090,10 +18960,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -27104,10 +18971,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -27117,78 +18981,48 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_count": { "description": "number of things with a particular property", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": [ - "number", - "null" - ] + "type": "number" }, "has_quotient": { - "type": [ - "number", - "null" - ] + "type": "number" }, "has_total": { "description": "total number of things in a particular reference set", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -27196,10 +19030,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -27207,24 +19038,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "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.", @@ -27232,37 +19054,25 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -27273,45 +19083,27 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -27319,61 +19111,40 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualified_predicate": { "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 \u2018full statement\u2019 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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject": { "description": "genotype that is associated with the phenotypic feature", @@ -27381,37 +19152,25 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -27422,35 +19181,23 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -27470,10 +19217,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -27484,10 +19228,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -27497,44 +19238,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -27542,10 +19268,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -27553,24 +19276,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "gene implicated in genotype", @@ -27578,75 +19292,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "the relationship type used to connect genotype to gene", @@ -27654,47 +19341,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "description": "parent genotype", @@ -27702,65 +19374,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -27790,34 +19441,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -27825,20 +19464,14 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -27846,56 +19479,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -27922,34 +19537,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -27957,20 +19560,14 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -27978,64 +19575,43 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -28062,34 +19638,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -28097,70 +19661,46 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "latitude": { "description": "latitude", - "type": [ - "number", - "null" - ] + "type": "number" }, "longitude": { "description": "longitude", - "type": [ - "number", - "null" - ] + "type": "number" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -28186,34 +19726,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -28221,78 +19749,51 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "latitude": { "description": "latitude", - "type": [ - "number", - "null" - ] + "type": "number" }, "longitude": { "description": "longitude", - "type": [ - "number", - "null" - ] + "type": "number" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -28318,34 +19819,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -28356,70 +19845,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -28445,41 +19910,26 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": [ - "string", - "null" - ] + "type": "string" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -28490,70 +19940,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -28579,34 +20005,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -28614,56 +20028,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -28695,34 +20091,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -28733,70 +20117,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -28822,34 +20182,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -28860,70 +20208,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -28939,10 +20263,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -28953,10 +20274,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -28966,44 +20284,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -29011,10 +20314,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -29022,24 +20322,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "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.", @@ -29047,75 +20338,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -29123,47 +20387,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "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.", @@ -29171,65 +20420,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -29259,34 +20487,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -29297,70 +20513,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -29379,10 +20571,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -29397,47 +20586,29 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": [ - "string", - "null" - ] + "type": "string" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "format": { - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "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.", @@ -29445,77 +20616,50 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iso_abbreviation": { "description": "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent.", - "type": [ - "string", - "null" - ] + "type": "string" }, "issue": { "description": "issue of a newspaper, a scientific journal or magazine for reference purpose", - "type": [ - "string", - "null" - ] + "type": "string" }, "keywords": { "description": "keywords tagging a publication", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "license": { - "type": [ - "string", - "null" - ] + "type": "string" }, "mesh_terms": { "description": "mesh terms tagging a publication", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "name": { "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).", - "type": [ - "string", - "null" - ] + "type": "string" }, "pages": { "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.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "publication_type": { "description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", @@ -29529,53 +20673,35 @@ "type": "string" }, "rights": { - "type": [ - "string", - "null" - ] + "type": "string" }, "summary": { "description": "executive summary of a publication", - "type": [ - "string", - "null" - ] + "type": "string" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "volume": { "description": "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication", - "type": [ - "string", - "null" - ] + "type": "string" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -29616,34 +20742,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -29654,70 +20768,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -29744,47 +20834,29 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": [ - "string", - "null" - ] + "type": "string" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "format": { - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -29792,68 +20864,44 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "license": { - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "rights": { - "type": [ - "string", - "null" - ] + "type": "string" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -29889,34 +20937,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -29927,70 +20963,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -30006,10 +21018,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -30020,10 +21029,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -30033,44 +21039,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -30078,10 +21069,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -30089,24 +21077,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "class describing the activity, process or localization of the gene product", @@ -30114,75 +21093,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -30190,47 +21142,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "$ref": "#/$defs/MacromolecularMachineMixin", @@ -30238,65 +21175,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -30316,10 +21232,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -30330,10 +21243,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -30343,44 +21253,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -30388,10 +21283,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -30399,24 +21291,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "class describing the activity, process or localization of the gene product", @@ -30424,75 +21307,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -30500,47 +21356,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "$ref": "#/$defs/MacromolecularMachineMixin", @@ -30548,65 +21389,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -30626,10 +21446,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -30640,10 +21457,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -30653,44 +21467,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -30698,10 +21497,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -30709,24 +21505,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "class describing the activity, process or localization of the gene product", @@ -30734,75 +21521,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -30810,47 +21570,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "$ref": "#/$defs/MacromolecularMachineMixin", @@ -30858,65 +21603,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -30946,34 +21670,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -30984,70 +21696,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -31073,34 +21761,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -31108,56 +21784,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -31173,10 +21831,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -31187,10 +21842,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -31200,44 +21852,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -31245,10 +21882,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -31256,24 +21890,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "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.", @@ -31281,75 +21906,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "derivation relationship", @@ -31357,47 +21955,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "description": "the material sample being described", @@ -31405,65 +21988,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -31483,10 +22045,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -31497,10 +22056,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -31510,44 +22066,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -31555,10 +22096,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -31566,24 +22104,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "disease or phenotype", @@ -31591,75 +22120,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -31667,47 +22169,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "description": "the material sample being described", @@ -31715,65 +22202,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -31817,34 +22283,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -31855,70 +22309,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -31944,64 +22374,43 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "enabled_by": { "description": "The gene product, gene, or complex that catalyzes the reaction", "items": { "$ref": "#/$defs/MacromolecularMachineMixin" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_input": { "description": "A chemical entity that is the input for the reaction", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_output": { "description": "A chemical entity that is the output for the reaction", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -32012,70 +22421,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -32091,10 +22476,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -32105,10 +22487,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -32118,44 +22497,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -32163,10 +22527,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -32174,24 +22535,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "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.", @@ -32199,75 +22551,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -32275,47 +22600,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "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.", @@ -32323,65 +22633,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -32401,10 +22690,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -32415,10 +22701,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -32428,44 +22711,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -32473,10 +22741,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -32484,24 +22749,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "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.", @@ -32509,75 +22765,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -32585,47 +22814,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "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.", @@ -32633,65 +22847,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -32711,10 +22904,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -32725,10 +22915,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -32738,44 +22925,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -32783,10 +22955,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -32794,24 +22963,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "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.", @@ -32819,75 +22979,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -32895,47 +23028,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "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.", @@ -32943,65 +23061,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -33024,10 +23121,7 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -33041,44 +23135,29 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -33086,84 +23165,54 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "is_metabolite": { "description": "indicates whether a molecular entity is a metabolite", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "is_toxic": { "description": "", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "max_tolerated_dose": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "trade_name": { "description": "", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -33182,10 +23231,7 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -33199,17 +23245,11 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "drug_regulatory_status_world_wide": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -33217,30 +23257,21 @@ }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "highest_FDA_approval_status": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -33252,94 +23283,61 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "is_supplement": { "description": "", - "type": [ - "string", - "null" - ] + "type": "string" }, "is_toxic": { "description": "", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "max_tolerated_dose": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "routes_of_delivery": { "description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": { "$ref": "#/$defs/DrugDeliveryEnum" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "trade_name": { "description": "", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -33371,34 +23369,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -33406,56 +23392,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -33471,10 +23439,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -33485,10 +23450,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -33498,44 +23460,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -33543,10 +23490,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -33554,24 +23498,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "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.", @@ -33579,95 +23514,59 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_context_qualifier": { - "type": [ - "string", - "null" - ] + "type": "string" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "population_context_qualifier": { "description": "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association.", - "type": [ - "string", - "null" - ] + "type": "string" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -33675,47 +23574,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "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.", @@ -33723,78 +23607,51 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_context_qualifier": { - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -33824,34 +23681,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -33862,70 +23707,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -33944,10 +23765,7 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -33961,51 +23779,33 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -34016,98 +23816,62 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "is_metabolite": { "description": "indicates whether a molecular entity is a metabolite", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "is_toxic": { "description": "", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "max_tolerated_dose": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "trade_name": { "description": "", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -34133,34 +23897,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -34171,70 +23923,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -34260,41 +23988,26 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": [ - "string", - "null" - ] + "type": "string" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -34305,70 +24018,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -34395,47 +24084,29 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": [ - "string", - "null" - ] + "type": "string" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "format": { - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -34443,68 +24114,44 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "license": { - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "rights": { - "type": [ - "string", - "null" - ] + "type": "string" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -34530,34 +24177,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -34565,20 +24200,14 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -34586,56 +24215,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -34662,34 +24273,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -34697,20 +24296,14 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -34718,56 +24311,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -34794,40 +24369,25 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_taxonomic_rank": { - "type": [ - "string", - "null" - ] + "type": "string" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -34835,56 +24395,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -34900,10 +24442,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -34914,17 +24453,11 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "associated_environmental_context": { "description": "the environment in which the two taxa interact", - "type": [ - "string", - "null" - ] + "type": "string" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -34934,44 +24467,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -34979,10 +24497,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -34990,24 +24505,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "the taxon that is the subject of the association", @@ -35015,75 +24521,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -35091,47 +24570,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "description": "the taxon that is the subject of the association", @@ -35139,65 +24603,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -35217,10 +24660,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -35231,10 +24671,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -35244,44 +24681,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -35289,10 +24711,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -35300,24 +24719,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "the more general taxon", @@ -35325,75 +24735,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -35401,47 +24784,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "description": "the more specific taxon", @@ -35449,65 +24817,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -35527,10 +24874,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -35541,10 +24885,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -35554,44 +24895,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -35599,10 +24925,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -35610,24 +24933,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "An association between two individual organisms.", @@ -35635,75 +24949,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -35711,47 +24998,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "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.", @@ -35759,65 +25031,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -35837,10 +25088,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -35851,10 +25099,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -35864,51 +25109,33 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -35916,10 +25143,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -35927,24 +25151,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "disease", @@ -35952,37 +25167,25 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -35993,45 +25196,27 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "The relationship to the disease", @@ -36039,54 +25224,36 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualified_predicate": { "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 \u2018full statement\u2019 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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "description": "A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease.", @@ -36094,37 +25261,25 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -36135,35 +25290,23 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -36183,10 +25326,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -36197,10 +25337,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -36210,44 +25347,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -36255,10 +25377,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -36266,24 +25385,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -36291,75 +25401,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "interaction relationship type", @@ -36367,47 +25450,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -36415,65 +25483,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -36493,10 +25540,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -36507,10 +25551,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -36520,61 +25561,40 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "identifier for the interaction. This may come from an interaction database such as IMEX.", "type": "string" }, "interacting_molecules_category": { - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -36582,24 +25602,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "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.", @@ -36607,75 +25618,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "interaction relationship type", @@ -36683,47 +25667,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "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.", @@ -36731,65 +25700,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -36812,10 +25760,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -36830,47 +25775,29 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": [ - "string", - "null" - ] + "type": "string" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "format": { - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "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.", @@ -36878,63 +25805,42 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "keywords": { "description": "keywords tagging a publication", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "license": { - "type": [ - "string", - "null" - ] + "type": "string" }, "mesh_terms": { "description": "mesh terms tagging a publication", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "name": { "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).", - "type": [ - "string", - "null" - ] + "type": "string" }, "pages": { "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.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "publication_type": { "description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", @@ -36944,46 +25850,31 @@ "type": "array" }, "rights": { - "type": [ - "string", - "null" - ] + "type": "string" }, "summary": { "description": "executive summary of a publication", - "type": [ - "string", - "null" - ] + "type": "string" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -37010,34 +25901,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -37045,20 +25924,14 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -37066,64 +25939,43 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -37156,34 +26008,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -37194,70 +26034,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -37283,64 +26099,43 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "enabled_by": { "description": "holds between a process and a physical entity, where the physical entity executes the process", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_input": { "description": "holds between a process and a continuant, where the continuant is an input into the process", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_output": { "description": "holds between a process and a continuant, where the continuant is an output of the process", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -37351,70 +26146,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -37440,34 +26211,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -37475,20 +26234,14 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -37496,64 +26249,43 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -37586,64 +26318,43 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "enabled_by": { "description": "holds between a process and a physical entity, where the physical entity executes the process", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_input": { "description": "holds between a process and a continuant, where the continuant is an input into the process", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_output": { "description": "holds between a process and a continuant, where the continuant is an output of the process", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -37654,70 +26365,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -37753,34 +26440,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -37788,56 +26463,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -37863,34 +26520,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -37901,70 +26546,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -37980,10 +26601,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -37994,10 +26612,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -38007,78 +26622,48 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_count": { "description": "number of things with a particular property", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": [ - "number", - "null" - ] + "type": "number" }, "has_quotient": { - "type": [ - "number", - "null" - ] + "type": "number" }, "has_total": { "description": "total number of things in a particular reference set", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -38086,10 +26671,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -38097,24 +26679,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "disease", @@ -38122,37 +26695,25 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -38163,45 +26724,27 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -38209,61 +26752,40 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualified_predicate": { "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 \u2018full statement\u2019 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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject": { "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.", @@ -38271,37 +26793,25 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -38312,35 +26822,23 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -38360,10 +26858,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -38374,10 +26869,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -38387,78 +26879,48 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_count": { "description": "number of things with a particular property", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": [ - "number", - "null" - ] + "type": "number" }, "has_quotient": { - "type": [ - "number", - "null" - ] + "type": "number" }, "has_total": { "description": "total number of things in a particular reference set", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -38466,10 +26928,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -38477,24 +26936,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "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.", @@ -38502,37 +26952,25 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -38543,45 +26981,27 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -38589,61 +27009,40 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualified_predicate": { "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 \u2018full statement\u2019 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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject": { "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.", @@ -38651,37 +27050,25 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -38692,35 +27079,23 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -38750,34 +27125,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -38785,20 +27148,14 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -38806,56 +27163,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -38882,34 +27221,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -38917,20 +27244,14 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -38938,56 +27259,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -39014,34 +27317,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -39049,56 +27340,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -39124,64 +27397,43 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "enabled_by": { "description": "holds between a process and a physical entity, where the physical entity executes the process", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_input": { "description": "holds between a process and a continuant, where the continuant is an input into the process", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_output": { "description": "holds between a process and a continuant, where the continuant is an output of the process", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -39192,70 +27444,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -39281,34 +27509,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -39316,56 +27532,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -39391,34 +27589,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -39429,70 +27615,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -39518,34 +27680,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -39556,70 +27706,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -39645,34 +27771,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -39683,70 +27797,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -39762,10 +27852,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -39776,10 +27863,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -39789,44 +27873,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -39834,10 +27903,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -39845,24 +27911,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "the population that form the object of the association", @@ -39870,75 +27927,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "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", @@ -39946,47 +27976,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "description": "the population that form the subject of the association", @@ -39994,65 +28009,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -40082,34 +28076,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -40120,70 +28102,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -40199,20 +28157,14 @@ "properties": { "anatomical_context_qualifier": { "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).", - "type": [ - "string", - "null" - ] + "type": "string" }, "broad_match": { "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.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "causal_mechanism_qualifier": { "$ref": "#/$defs/CausalMechanismQualifierEnum", @@ -40223,47 +28175,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "mapped_predicate": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "narrow_match": { "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.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_context_qualifier": { - "type": [ - "string", - "null" - ] + "type": "string" }, "object_derivative_qualifier": { "description": "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier \u2018metabolite\u2019 combines with a \u2018Chemical X\u2019 core concept to express the composed concept \u2018a metabolite of Chemical X\u2019. This qualifier is for the object of an association (or statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -40271,17 +28205,11 @@ }, "object_form_or_variant_qualifier": { "description": "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier \u2018mutation\u2019 combines with the core concept \u2018Gene X\u2019 to express the compose concept \u2018a mutation of Gene X\u2019. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_part_qualifier": { "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -40289,37 +28217,22 @@ }, "qualified_predicate": { "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 \u2018full statement\u2019 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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "species_context_qualifier": { "description": "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_context_qualifier": { - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_derivative_qualifier": { "description": "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier \u2018metabolite\u2019 combines with a \u2018Chemical X\u2019 core concept to express the composed concept \u2018a metabolite of Chemical X\u2019. This qualifier is for the subject of an association (or statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -40327,17 +28240,11 @@ }, "subject_form_or_variant_qualifier": { "description": "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier \u2018mutation\u2019 combines with the core concept \u2018Gene X\u2019 to express the compose concept \u2018a mutation of Gene X\u2019. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_part_qualifier": { "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement).", - "type": [ - "string", - "null" - ] + "type": "string" } }, "required": [ @@ -40355,10 +28262,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -40373,47 +28277,29 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": [ - "string", - "null" - ] + "type": "string" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "format": { - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "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.", @@ -40421,63 +28307,42 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "keywords": { "description": "keywords tagging a publication", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "license": { - "type": [ - "string", - "null" - ] + "type": "string" }, "mesh_terms": { "description": "mesh terms tagging a publication", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "name": { "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).", - "type": [ - "string", - "null" - ] + "type": "string" }, "pages": { "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.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "publication_type": { "description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", @@ -40487,46 +28352,31 @@ "type": "array" }, "rights": { - "type": [ - "string", - "null" - ] + "type": "string" }, "summary": { "description": "executive summary of a publication", - "type": [ - "string", - "null" - ] + "type": "string" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -40553,34 +28403,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -40588,56 +28426,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -40653,10 +28473,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -40667,10 +28484,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -40680,44 +28494,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -40725,10 +28524,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -40736,24 +28532,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "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.", @@ -40761,75 +28548,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -40837,47 +28597,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "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.", @@ -40885,65 +28630,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -40966,10 +28690,7 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -40983,17 +28704,11 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "drug_regulatory_status_world_wide": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -41001,30 +28716,21 @@ }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "highest_FDA_approval_status": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -41036,94 +28742,61 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "is_supplement": { "description": "", - "type": [ - "string", - "null" - ] + "type": "string" }, "is_toxic": { "description": "", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "max_tolerated_dose": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "routes_of_delivery": { "description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": { "$ref": "#/$defs/DrugDeliveryEnum" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "trade_name": { "description": "", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -41149,34 +28822,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -41187,70 +28848,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -41276,44 +28913,29 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_gene_or_gene_product": { "description": "connects an entity with one or more gene or gene products", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -41324,70 +28946,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -41413,44 +29011,29 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_gene_or_gene_product": { "description": "connects an entity with one or more gene or gene products", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -41461,70 +29044,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -41550,34 +29109,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -41588,70 +29135,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -41670,10 +29193,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -41688,47 +29208,29 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": [ - "string", - "null" - ] + "type": "string" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "format": { - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "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.", @@ -41736,63 +29238,42 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "keywords": { "description": "keywords tagging a publication", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "license": { - "type": [ - "string", - "null" - ] + "type": "string" }, "mesh_terms": { "description": "mesh terms tagging a publication", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "name": { "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).", - "type": [ - "string", - "null" - ] + "type": "string" }, "pages": { "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.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "publication_type": { "description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", @@ -41802,46 +29283,31 @@ "type": "array" }, "rights": { - "type": [ - "string", - "null" - ] + "type": "string" }, "summary": { "description": "executive summary of a publication", - "type": [ - "string", - "null" - ] + "type": "string" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -41858,17 +29324,11 @@ "properties": { "has_numeric_value": { "description": "connects a quantity value to a number", - "type": [ - "number", - "null" - ] + "type": "number" }, "has_unit": { "description": "connects a quantity value to a unit", - "type": [ - "string", - "null" - ] + "type": "string" } }, "title": "QuantityValue", @@ -41890,34 +29350,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -41928,70 +29376,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -42017,34 +29441,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -42055,70 +29467,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -42154,10 +29542,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -42168,10 +29553,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -42181,44 +29563,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -42226,10 +29593,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -42237,24 +29601,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -42262,75 +29617,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -42338,37 +29666,25 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "reaction_direction": { "$ref": "#/$defs/ReactionDirectionEnum", @@ -42383,17 +29699,11 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "stoichiometry": { "description": "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers.", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "subject": { "description": "the chemical entity or entity that is an interactor", @@ -42401,65 +29711,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -42479,10 +29768,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -42493,10 +29779,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -42506,44 +29789,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -42551,10 +29819,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -42562,24 +29827,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "the chemical element that is the target of the statement", @@ -42587,75 +29843,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -42663,37 +29892,25 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "reaction_direction": { "$ref": "#/$defs/ReactionDirectionEnum", @@ -42708,17 +29925,11 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "stoichiometry": { "description": "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers.", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "subject": { "description": "the chemical entity or entity that is an interactor", @@ -42726,65 +29937,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -42814,41 +30004,26 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": [ - "string", - "null" - ] + "type": "string" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -42859,70 +30034,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -42948,41 +30099,26 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": [ - "string", - "null" - ] + "type": "string" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -42993,70 +30129,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -43098,47 +30210,29 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": [ - "string", - "null" - ] + "type": "string" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "format": { - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -43146,68 +30240,44 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "license": { - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "rights": { - "type": [ - "string", - "null" - ] + "type": "string" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -43244,47 +30314,29 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": [ - "string", - "null" - ] + "type": "string" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "format": { - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -43292,33 +30344,21 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "license": { - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "resource_id": { "description": "The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge.", @@ -43329,46 +30369,31 @@ "description": "The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge." }, "rights": { - "type": [ - "string", - "null" - ] + "type": "string" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "upstream_resource_ids": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -43386,10 +30411,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -43400,10 +30422,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -43413,44 +30432,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -43458,10 +30462,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -43469,24 +30470,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "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.", @@ -43494,75 +30486,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -43570,47 +30535,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "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.", @@ -43618,65 +30568,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -43705,10 +30634,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -43719,10 +30645,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -43732,44 +30655,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -43777,10 +30685,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -43788,24 +30693,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "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.", @@ -43813,75 +30709,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -43889,47 +30758,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "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.", @@ -43937,65 +30791,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -44025,51 +30858,33 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_biological_sequence": { "description": "The state of the sequence w.r.t a reference sequence", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_gene": { "description": "Each allele can be associated with any number of genes", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -44080,70 +30895,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -44162,10 +30953,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -44180,47 +30968,29 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": [ - "string", - "null" - ] + "type": "string" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "format": { - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "Serials (journals) should have industry-standard identifier such as from ISSN.", @@ -44228,77 +30998,50 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iso_abbreviation": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "issue": { "description": "issue of a newspaper, a scientific journal or magazine for reference purpose", - "type": [ - "string", - "null" - ] + "type": "string" }, "keywords": { "description": "keywords tagging a publication", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "license": { - "type": [ - "string", - "null" - ] + "type": "string" }, "mesh_terms": { "description": "mesh terms tagging a publication", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "name": { "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).", - "type": [ - "string", - "null" - ] + "type": "string" }, "pages": { "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.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "publication_type": { "description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", @@ -44308,54 +31051,36 @@ "type": "array" }, "rights": { - "type": [ - "string", - "null" - ] + "type": "string" }, "summary": { "description": "executive summary of a publication", - "type": [ - "string", - "null" - ] + "type": "string" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "description": "Should generally be set to an ontology class defined term for 'serial' or 'journal'.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "volume": { "description": "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication", - "type": [ - "string", - "null" - ] + "type": "string" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -44382,34 +31107,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -44417,20 +31130,14 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -44438,56 +31145,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -44514,34 +31203,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -44552,70 +31229,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -44634,10 +31287,7 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -44651,44 +31301,29 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -44696,84 +31331,54 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "is_metabolite": { "description": "indicates whether a molecular entity is a metabolite", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "is_toxic": { "description": "", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "max_tolerated_dose": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "trade_name": { "description": "", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -44799,51 +31404,33 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_biological_sequence": { "description": "The state of the sequence w.r.t a reference sequence", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_gene": { "description": "Each allele can be associated with any number of genes", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -44854,70 +31441,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -44943,34 +31506,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -44978,20 +31529,14 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -44999,56 +31544,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -45075,24 +31602,15 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", @@ -45107,20 +31625,14 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -45128,64 +31640,43 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -45230,34 +31721,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -45265,56 +31744,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -45340,34 +31801,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -45378,70 +31827,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -45468,47 +31893,29 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": [ - "string", - "null" - ] + "type": "string" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "format": { - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -45516,68 +31923,44 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "license": { - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "rights": { - "type": [ - "string", - "null" - ] + "type": "string" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -45593,10 +31976,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -45607,10 +31987,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -45620,44 +31997,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -45665,10 +32027,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -45676,24 +32035,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "An association between individuals of different taxa.", @@ -45701,75 +32051,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -45777,47 +32100,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "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.", @@ -45825,65 +32133,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -45929,47 +32216,29 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": [ - "string", - "null" - ] + "type": "string" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "format": { - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -45977,68 +32246,44 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "license": { - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "rights": { - "type": [ - "string", - "null" - ] + "type": "string" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -46064,34 +32309,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -46102,70 +32335,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -46181,10 +32390,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -46195,10 +32401,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -46208,44 +32411,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -46253,10 +32441,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -46264,24 +32449,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "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.", @@ -46289,75 +32465,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -46365,47 +32514,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "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.", @@ -46413,65 +32547,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -46501,41 +32614,26 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": [ - "string", - "null" - ] + "type": "string" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -46546,70 +32644,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -46635,64 +32709,43 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_device": { "description": "connects an entity to one or more (medical) devices", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_drug": { "description": "connects an entity to one or more drugs", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_procedure": { "description": "connects an entity to one or more (medical) procedures", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -46700,64 +32753,43 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -46773,10 +32805,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -46787,10 +32816,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -46800,51 +32826,33 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -46852,10 +32860,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -46863,24 +32868,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "disease", @@ -46888,37 +32884,25 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -46929,45 +32913,27 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "The relationship to the disease", @@ -46975,54 +32941,36 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualified_predicate": { "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 \u2018full statement\u2019 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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "description": "A variant that has a role in modeling the disease.", @@ -47030,37 +32978,25 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -47071,35 +33007,23 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -47119,10 +33043,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -47133,10 +33054,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -47146,51 +33064,33 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -47198,10 +33098,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -47209,24 +33106,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "a disease that is associated with that variant", @@ -47234,37 +33122,25 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -47275,45 +33151,27 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "E.g. is pathogenic for", @@ -47321,54 +33179,36 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualified_predicate": { "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 \u2018full statement\u2019 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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "description": "a sequence variant in which the allele state is associated in some way with the disease state", @@ -47376,37 +33216,25 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -47417,35 +33245,23 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -47465,10 +33281,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -47479,10 +33292,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -47492,44 +33302,29 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -47537,10 +33332,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -47548,24 +33340,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "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.", @@ -47573,75 +33356,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -47649,47 +33405,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "description": "a sequence variant in which the allele state is associated with some other entity", @@ -47697,65 +33438,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -47775,10 +33495,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -47789,10 +33506,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -47802,51 +33516,33 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "expression_site": { "description": "location in which gene or protein expression takes place. May be cell, tissue, or organ.", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -47854,10 +33550,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -47865,24 +33558,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "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.", @@ -47890,82 +33574,52 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "phenotypic_state": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -47973,61 +33627,40 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "quantifier_qualifier": { "description": "Optional quantitative value indicating degree of expression.", - "type": [ - "string", - "null" - ] + "type": "string" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "stage_qualifier": { "description": "stage during which gene or protein expression of takes place.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject": { "description": "a sequence variant in which the allele state is associated with some other entity", @@ -48035,65 +33668,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -48113,10 +33725,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -48127,10 +33736,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -48140,78 +33746,48 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_count": { "description": "number of things with a particular property", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": [ - "number", - "null" - ] + "type": "number" }, "has_quotient": { - "type": [ - "number", - "null" - ] + "type": "number" }, "has_total": { "description": "total number of things in a particular reference set", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -48219,10 +33795,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -48230,24 +33803,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "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.", @@ -48255,37 +33819,25 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -48296,45 +33848,27 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -48342,61 +33876,40 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualified_predicate": { "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 \u2018full statement\u2019 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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject": { "description": "a sequence variant in which the allele state is associated in some way with the phenotype state", @@ -48404,37 +33917,25 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -48445,35 +33946,23 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -48493,10 +33982,7 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": [ - "number", - "null" - ] + "type": "number" }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -48507,10 +33993,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -48520,79 +34003,49 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_count": { "description": "number in object population that carry a particular allele, aka allele count", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": [ - "number", - "null" - ] + "type": "number" }, "has_quotient": { "description": "frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency", - "type": [ - "number", - "null" - ] + "type": "number" }, "has_total": { "description": "number all populations that carry a particular allele, aka allele number", - "type": [ - "integer", - "null" - ] + "type": "integer" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -48600,10 +34053,7 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -48611,24 +34061,15 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "object": { "description": "the population that is observed to have the frequency", @@ -48636,75 +34077,48 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": [ - "string", - "null" - ] + "type": "string" }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": [ - "number", - "null" - ] + "type": "number" }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -48712,47 +34126,32 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": [ - "string", - "null" - ] + "type": "string" }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": [ - "string", - "null" - ] + "type": "string" }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject": { "description": "an allele that has a certain frequency in a given population", @@ -48760,65 +34159,44 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": [ - "string", - "null" - ] + "type": "string" }, "timepoint": { "description": "a point in time", "format": "time", - "type": [ - "string", - "null" - ] + "type": "string" }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -48848,34 +34226,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -48886,70 +34252,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -48975,34 +34317,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -49013,70 +34343,46 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -49095,10 +34401,7 @@ "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -49113,47 +34416,29 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": [ - "string", - "null" - ] + "type": "string" }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "format": { - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "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.", @@ -49161,63 +34446,42 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "keywords": { "description": "keywords tagging a publication", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "license": { - "type": [ - "string", - "null" - ] + "type": "string" }, "mesh_terms": { "description": "mesh terms tagging a publication", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "name": { "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).", - "type": [ - "string", - "null" - ] + "type": "string" }, "pages": { "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.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "publication_type": { "description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", @@ -49227,46 +34491,31 @@ "type": "array" }, "rights": { - "type": [ - "string", - "null" - ] + "type": "string" }, "summary": { "description": "executive summary of a publication", - "type": [ - "string", - "null" - ] + "type": "string" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ @@ -49293,34 +34542,22 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": [ - "boolean", - "null" - ] + "type": "boolean" }, "description": { "description": "a human-readable description of an entity", - "type": [ - "string", - "null" - ] + "type": "string" }, "full_name": { "description": "a long-form human readable name for a thing", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -49328,20 +34565,14 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": [ - "string", - "null" - ] + "type": "string" }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -49349,56 +34580,38 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": [ - "string", - "null" - ] + "type": "string" }, "name": { "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.", - "type": [ - "string", - "null" - ] + "type": "string" }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "type": { "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": [ - "array", - "null" - ] + "type": "array" } }, "required": [ diff --git a/project/owl/biolink_model.owl.ttl b/project/owl/biolink_model.owl.ttl index 21e6c07e7..a3c5cdbf0 100644 --- a/project/owl/biolink_model.owl.ttl +++ b/project/owl/biolink_model.owl.ttl @@ -2597,13 +2597,13 @@ biolink:AccessibleDnaRegion a owl:Class ; owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], biolink:RegulatoryRegion ; skos:altLabel "atac-seq accessible region", "dnase-seq accessible region" ; @@ -2649,32 +2649,32 @@ biolink:AccessibleDnaRegion a owl:Class ; biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity ontogenic association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:AnatomicalEntityToAnatomicalEntityAssociation ; skos:definition "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship." ; skos:inScheme . @@ -2684,30 +2684,30 @@ biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:AnatomicalEntityToAnatomicalEntityAssociation ; skos:definition "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms" ; skos:inScheme . @@ -2798,26 +2798,26 @@ biolink:Bacterium a owl:Class ; biolink:BehaviorToBehavioralFeatureAssociation a owl:Class ; rdfs:label "behavior to behavioral feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:BehavioralFeature ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:Behavior ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:BehavioralFeature ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior." ; skos:inScheme . @@ -2845,6 +2845,12 @@ biolink:BioticExposure a owl:Class ; biolink:Book a owl:Class ; rdfs:label "book" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:type ], + [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:id ], [ a owl:Restriction ; @@ -2853,12 +2859,6 @@ biolink:Book a owl:Class ; [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:type ], biolink:Publication ; skos:definition "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; skos:inScheme . @@ -2873,10 +2873,10 @@ biolink:CaseToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "case to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:CaseToEntityAssociationMixin ], + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:someValuesFrom biolink:CaseToEntityAssociationMixin ], biolink:Association ; skos:definition "An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype." ; skos:inScheme . @@ -2886,27 +2886,27 @@ biolink:CausalGeneToDiseaseAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Disease ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], biolink:GeneToDiseaseAssociation ; skos:inScheme . @@ -3000,19 +3000,19 @@ biolink:CellLineAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "cell line as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:CellLine ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation ; skos:inScheme . @@ -3026,166 +3026,166 @@ biolink:ChemicalAffectsGeneAssociation a owl:Class ; rdfs:label "chemical affects gene association" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:species_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:causal_mechanism_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:anatomical_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:species_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:minCardinality 0 ; owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:object_context_qualifier ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; owl:onProperty biolink:subject_derivative_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:object_part_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:causal_mechanism_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; + owl:minCardinality 0 ; owl:onProperty biolink:subject_derivative_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:anatomical_context_qualifier ], biolink:Association ; skos:definition "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)" ; skos:inScheme . @@ -3193,29 +3193,29 @@ biolink:ChemicalAffectsGeneAssociation a owl:Class ; biolink:ChemicalEntityAssessesNamedThingAssociation a owl:Class ; rdfs:label "chemical entity assesses named thing association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], @@ -3225,41 +3225,41 @@ biolink:ChemicalEntityAssessesNamedThingAssociation a owl:Class ; biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a owl:Class ; rdfs:label "chemical entity or gene or gene product regulates gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "A regulatory relationship between two genes" ; skos:inScheme . @@ -3267,7 +3267,19 @@ biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a owl:Class ; biolink:ChemicalGeneInteractionAssociation a owl:Class ; rdfs:label "chemical gene interaction association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_derivative_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:object_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; @@ -3275,99 +3287,87 @@ biolink:ChemicalGeneInteractionAssociation a owl:Class ; [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; + owl:minCardinality 0 ; owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:subject_part_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_part_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:Association ; 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)" ; skos:exactMatch SIO:001257 ; @@ -3376,19 +3376,19 @@ biolink:ChemicalGeneInteractionAssociation a owl:Class ; biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "chemical or drug or treatment side effect disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation ; skos:definition "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." ; @@ -3417,38 +3417,38 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation biolink:ChemicalToChemicalDerivationAssociation a owl:Class ; rdfs:label "chemical to chemical derivation association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:minCardinality 0 ; owl:onProperty biolink:catalyst_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:MacromolecularMachineMixin ; owl:onProperty biolink:catalyst_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], biolink:ChemicalToChemicalAssociation ; skos:definition "A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: IF R has-input C1 AND R has-output C2 AND R enabled-by P AND R type Reaction THEN C1 derives-into C2 catalyst qualifier P" ; skos:inScheme . @@ -3456,17 +3456,17 @@ biolink:ChemicalToChemicalDerivationAssociation a owl:Class ; biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "chemical to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], @@ -3478,23 +3478,23 @@ biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; biolink:ChemicalToPathwayAssociation a owl:Class ; rdfs:label "chemical to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:Pathway ; owl:onProperty biolink:object ], @@ -3544,13 +3544,13 @@ biolink:ClinicalFinding a owl:Class ; biolink:ClinicalMeasurement a owl:Class ; rdfs:label "clinical measurement" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; + owl:minCardinality 1 ; owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom owl:Thing ; owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_attribute_type ], biolink:ClinicalAttribute ; skos:definition "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." ; @@ -3604,38 +3604,38 @@ biolink:ConceptCountAnalysisResult a owl:Class ; biolink:ContributorAssociation a owl:Class ; rdfs:label "contributor association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:InformationContentEntity ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; owl:onProperty biolink:qualifiers ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:Agent ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:minCardinality 0 ; + owl:onProperty biolink:qualifiers ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:InformationContentEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - 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" ; skos:inScheme . @@ -3646,26 +3646,26 @@ biolink:CorrelatedGeneToDiseaseAssociation a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], biolink:GeneToDiseaseAssociation ; skos:inScheme . @@ -3694,17 +3694,17 @@ biolink:DiseaseOrPhenotypicFeatureExposure a owl:Class ; biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a owl:Class ; rdfs:label "disease or phenotypic feature to genetic inheritance association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneticInheritance ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneticInheritance ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], @@ -3712,8 +3712,8 @@ biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin ], biolink:Association ; skos:definition "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance." ; skos:inScheme . @@ -3721,17 +3721,17 @@ biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a owl:Class ; biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a owl:Class ; rdfs:label "disease or phenotypic feature to location association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site." ; skos:inScheme . @@ -3740,10 +3740,10 @@ biolink:DiseaseToExposureEventAssociation a owl:Class ; rdfs:label "disease to exposure event association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToExposureEventAssociationMixin ], + owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin ], + owl:someValuesFrom biolink:EntityToExposureEventAssociationMixin ], biolink:Association ; skos:definition "An association between an exposure event and a disease." ; skos:inScheme . @@ -3751,41 +3751,41 @@ biolink:DiseaseToExposureEventAssociation a owl:Class ; biolink:DiseaseToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "disease to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:PhenotypicFeature ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], + owl:allValuesFrom biolink:PhenotypicFeature ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Onset ; owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:someValuesFrom biolink:FrequencyQuantifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:Disease ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQuantifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:onset_qualifier ], biolink:Association ; skos:closeMatch dcid:DiseaseSymptomAssociation ; skos:definition "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." ; @@ -3842,12 +3842,12 @@ biolink:DrugToGeneAssociation a owl:Class ; [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:DrugToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An interaction between a drug and a gene or gene product." ; skos:inScheme ; @@ -3885,58 +3885,58 @@ biolink:DrugToGeneInteractionExposure a owl:Class ; biolink:DruggableGeneToDiseaseAssociation a owl:Class ; rdfs:label "druggable gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_evidence ], - [ a owl:Restriction ; owl:allValuesFrom biolink:DruggableGeneCategoryEnum ; owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], biolink:GeneToDiseaseAssociation ; skos:inScheme . biolink:EntityToDiseaseAssociation a owl:Class ; rdfs:label "entity to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:MaxResearchPhaseEnum ; - owl:onProperty biolink:max_research_phase ], + owl:maxCardinality 1 ; + owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:clinical_approval_status ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:max_research_phase ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:max_research_phase ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ; owl:onProperty biolink:clinical_approval_status ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MaxResearchPhaseEnum ; + owl:onProperty biolink:max_research_phase ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:max_research_phase ], biolink:Association ; skos:inScheme . @@ -3955,9 +3955,6 @@ biolink:EntityToOutcomeAssociationMixin a owl:Class ; biolink:EntityToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "entity to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:clinical_approval_status ], - [ a owl:Restriction ; owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ; owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; @@ -3967,11 +3964,14 @@ biolink:EntityToPhenotypicFeatureAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:max_research_phase ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MaxResearchPhaseEnum ; - owl:onProperty biolink:max_research_phase ], + owl:maxCardinality 1 ; + owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:max_research_phase ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MaxResearchPhaseEnum ; + owl:onProperty biolink:max_research_phase ], biolink:Association ; skos:inScheme . @@ -4017,9 +4017,6 @@ biolink:ExonToTranscriptRelationship a owl:Class ; [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:Transcript ; owl:onProperty biolink:object ], @@ -4029,6 +4026,9 @@ biolink:ExonToTranscriptRelationship a owl:Class ; [ a owl:Restriction ; owl:allValuesFrom biolink:Exon ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], biolink:SequenceFeatureRelationship ; skos:definition "A transcript is formed from multiple exons" ; skos:inScheme . @@ -4037,10 +4037,13 @@ biolink:ExposureEventToOutcomeAssociation a owl:Class ; rdfs:label "exposure event to outcome association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:temporal_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:temporal_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:time ; owl:onProperty biolink:temporal_context_qualifier ], @@ -4048,14 +4051,11 @@ biolink:ExposureEventToOutcomeAssociation a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToOutcomeAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; + owl:minCardinality 0 ; owl:onProperty biolink:population_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:temporal_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:population_context_qualifier ], + owl:onProperty biolink:temporal_context_qualifier ], biolink:Association ; skos:definition "An association between an exposure event and an outcome." ; skos:inScheme . @@ -4063,17 +4063,17 @@ biolink:ExposureEventToOutcomeAssociation a owl:Class ; biolink:ExposureEventToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "exposure event to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:ExposureEvent ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], biolink:Association ; skos:definition "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." ; skos:inScheme . @@ -4131,175 +4131,175 @@ biolink:GeneAffectsChemicalAssociation a owl:Class ; rdfs:label "gene affects chemical association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:species_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:causal_mechanism_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:species_context_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:anatomical_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_part_qualifier ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_part_qualifier ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:species_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:object_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_derivative_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:anatomical_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:minCardinality 0 ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_derivative_qualifier ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:causal_mechanism_qualifier ], biolink:Association ; skos:definition "Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, activity, localization, processing, transport, etc.)" ; skos:inScheme . @@ -4307,6 +4307,12 @@ biolink:GeneAffectsChemicalAssociation a owl:Class ; biolink:GeneAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "gene as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; @@ -4315,53 +4321,47 @@ biolink:GeneAsAModelOfDiseaseAssociation a owl:Class ; [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], biolink:GeneToDiseaseAssociation ; skos:inScheme . biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ; rdfs:label "gene has variant that contributes to disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:object ], biolink:GeneToDiseaseAssociation ; skos:inScheme . @@ -4648,68 +4648,68 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ; biolink:GeneRegulatesGeneAssociation a owl:Class ; rdfs:label "gene regulates gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; + owl:maxCardinality 1 ; owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:maxCardinality 1 ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:species_context_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object_aspect_qualifier ], biolink:Association ; skos:definition "Describes a regulatory relationship between two genes or gene products." ; skos:inScheme . @@ -4718,50 +4718,50 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; rdfs:label "gene to expression site association" ; rdfs:seeAlso ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:stage_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "An association between a gene and a gene expression site, possibly qualified by stage/timing info." ; skos:editorialNote "TBD: introduce subclasses for distinction between wild-type and experimental conditions?" ; @@ -4770,16 +4770,16 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; biolink:GeneToGeneCoexpressionAssociation a owl:Class ; rdfs:label "gene to gene coexpression association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneExpressionMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], biolink:GeneToGeneAssociation ; skos:definition "Indicates that two genes are co-expressed, generally under the same conditions." ; @@ -4788,32 +4788,32 @@ biolink:GeneToGeneCoexpressionAssociation a owl:Class ; biolink:GeneToGeneFamilyAssociation a owl:Class ; rdfs:label "gene to gene family association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneFamily ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:GeneFamily ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:subject ], 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." ; skos:inScheme . @@ -4821,32 +4821,32 @@ biolink:GeneToGeneFamilyAssociation a owl:Class ; biolink:GeneToGeneHomologyAssociation a owl:Class ; rdfs:label "gene to gene homology association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], 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)" ; skos:inScheme . @@ -4857,29 +4857,29 @@ biolink:GeneToGeneProductRelationship a owl:Class ; owl:allValuesFrom biolink:GeneProductMixin ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:subject ], biolink:SequenceFeatureRelationship ; skos:definition "A gene is transcribed and potentially translated to a gene product" ; skos:inScheme . @@ -4887,20 +4887,20 @@ biolink:GeneToGeneProductRelationship a owl:Class ; biolink:GeneToGoTermAssociation a owl:Class ; rdfs:label "gene to go term association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], @@ -4915,22 +4915,22 @@ biolink:GeneToPathwayAssociation a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:Pathway ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Pathway ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], biolink:Association ; skos:definition "An interaction between a gene or gene product and a biological process or pathway." ; @@ -4939,29 +4939,29 @@ biolink:GeneToPathwayAssociation a owl:Class ; biolink:GeneToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "gene to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:PhenotypicFeature ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:PhenotypicFeature ; + owl:onProperty biolink:object ], biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; skos:exactMatch WBVocab:Gene-Phenotype-Association ; skos:inScheme . @@ -4973,10 +4973,10 @@ biolink:Genome a owl:Class ; owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:OntologyClass ], biolink:BiologicalEntity ; skos:closeMatch dcid:GenomeAssemblyUnit ; skos:definition "A genome is the sum of genetic material within a cell or virion." ; @@ -4992,19 +4992,19 @@ biolink:GenomicBackgroundExposure a owl:Class ; owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneGroupingMixin ], + owl:someValuesFrom biolink:ThingWithTaxon ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:GeneGroupingMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ExposureEvent ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ThingWithTaxon ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:ExposureEvent ], biolink:Attribute ; skos:definition "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." ; skos:inScheme . @@ -5012,17 +5012,17 @@ biolink:GenomicBackgroundExposure a owl:Class ; biolink:GenotypeAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "genotype as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], @@ -5032,32 +5032,32 @@ biolink:GenotypeAsAModelOfDiseaseAssociation a owl:Class ; biolink:GenotypeToGeneAssociation a owl:Class ; rdfs:label "genotype to gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], 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" ; skos:inScheme . @@ -5065,16 +5065,16 @@ biolink:GenotypeToGeneAssociation a owl:Class ; biolink:GenotypeToGenotypePartAssociation a owl:Class ; rdfs:label "genotype to genotype part association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; @@ -5083,11 +5083,11 @@ biolink:GenotypeToGenotypePartAssociation a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:Genotype ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], @@ -5098,29 +5098,29 @@ biolink:GenotypeToGenotypePartAssociation a owl:Class ; biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "genotype to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment" ; skos:inScheme . @@ -5128,20 +5128,14 @@ biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; biolink:GenotypeToVariantAssociation a owl:Class ; rdfs:label "genotype to variant association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], @@ -5149,11 +5143,17 @@ biolink:GenotypeToVariantAssociation a owl:Class ; owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:SequenceVariant ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], biolink:Association ; skos:definition "Any association between a genotype and a sequence variant." ; skos:inScheme . @@ -5195,10 +5195,10 @@ biolink:GeographicLocationAtTime a owl:Class ; owl:minCardinality 0 ; owl:onProperty biolink:timepoint ], [ a owl:Restriction ; - owl:allValuesFrom xsd:time ; + owl:maxCardinality 1 ; owl:onProperty biolink:timepoint ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:time ; owl:onProperty biolink:timepoint ], biolink:GeographicLocation ; skos:definition "a location that can be described in lat/long coordinates, for a particular time" ; @@ -5220,13 +5220,13 @@ biolink:Haplotype a owl:Class ; rdfs:label "haplotype" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:PhysicalEssence ], biolink:BiologicalEntity ; skos:definition "A set of zero or more Alleles on a single instance of a Sequence[VMC]" ; skos:exactMatch , @@ -5257,32 +5257,32 @@ biolink:Human a owl:Class ; biolink:InformationContentEntityToNamedThingAssociation a owl:Class ; rdfs:label "information content entity to named thing association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property)." ; skos:inScheme . @@ -5361,14 +5361,14 @@ biolink:MacromolecularComplex a owl:Class ; biolink:MacromolecularMachineToBiologicalProcessAssociation a owl:Class ; rdfs:label "macromolecular machine to biological process association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:BiologicalProcess ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], @@ -5382,13 +5382,13 @@ biolink:MacromolecularMachineToCellularComponentAssociation a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:CellularComponent ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:CellularComponent ; owl:onProperty biolink:object ], biolink:FunctionalAssociation ; skos:definition "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." ; @@ -5397,16 +5397,16 @@ biolink:MacromolecularMachineToCellularComponentAssociation a owl:Class ; biolink:MacromolecularMachineToMolecularActivityAssociation a owl:Class ; rdfs:label "macromolecular machine to molecular activity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularActivity ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:MolecularActivity ; owl:onProperty biolink:object ], biolink:FunctionalAssociation ; skos:definition "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." ; @@ -5416,31 +5416,31 @@ biolink:MaterialSampleDerivationAssociation a owl:Class ; rdfs:label "material sample derivation association" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:MaterialSample ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between a material sample and the material entity from which it is derived." ; skos:inScheme . @@ -5449,10 +5449,10 @@ biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "material sample to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], + owl:someValuesFrom biolink:MaterialSampleToEntityAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MaterialSampleToEntityAssociationMixin ], + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], biolink:Association ; skos:definition "An association between a material sample and a disease or phenotype." ; skos:inScheme . @@ -5507,20 +5507,20 @@ biolink:MolecularActivityToChemicalEntityAssociation a owl:Class ; owl:allValuesFrom biolink:MolecularActivity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], 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" ; skos:inScheme . @@ -5528,23 +5528,23 @@ biolink:MolecularActivityToChemicalEntityAssociation a owl:Class ; biolink:MolecularActivityToMolecularActivityAssociation a owl:Class ; rdfs:label "molecular activity to molecular activity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:MolecularActivity ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularActivity ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularActivity ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], 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" ; skos:inScheme . @@ -5552,32 +5552,32 @@ biolink:MolecularActivityToMolecularActivityAssociation a owl:Class ; biolink:MolecularActivityToPathwayAssociation a owl:Class ; rdfs:label "molecular activity to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularActivity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:Pathway ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Pathway ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Association that holds the relationship between a reaction and the pathway it participates in." ; skos:inScheme . @@ -5585,77 +5585,77 @@ biolink:MolecularActivityToPathwayAssociation a owl:Class ; biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a owl:Class ; rdfs:label "named thing associated with likelihood of named thing association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; - owl:onProperty biolink:population_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:object_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:population_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:population_context_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; + owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ], biolink:Association ; skos:inScheme . @@ -5673,10 +5673,10 @@ biolink:NucleosomeModification a owl:Class ; owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneProductIsoformMixin ], + owl:someValuesFrom biolink:EpigenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EpigenomicEntity ], + owl:someValuesFrom biolink:GeneProductIsoformMixin ], biolink:BiologicalEntity ; skos:definition "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." ; skos:inScheme . @@ -5690,35 +5690,35 @@ biolink:ObservedExpectedFrequencyAnalysisResult a owl:Class ; biolink:OrganismTaxonToEnvironmentAssociation a owl:Class ; rdfs:label "organism taxon to environment association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ], - [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom owl:Thing ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ], biolink:Association ; skos:inScheme . @@ -5726,39 +5726,39 @@ biolink:OrganismTaxonToOrganismTaxonInteraction a owl:Class ; rdfs:label "organism taxon to organism taxon interaction" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:associated_environmental_context ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:associated_environmental_context ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:associated_environmental_context ], + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:associated_environmental_context ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:associated_environmental_context ], biolink:OrganismTaxonToOrganismTaxonAssociation ; skos:definition "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" ; @@ -5767,31 +5767,31 @@ biolink:OrganismTaxonToOrganismTaxonInteraction a owl:Class ; biolink:OrganismTaxonToOrganismTaxonSpecialization a owl:Class ; rdfs:label "organism taxon to organism taxon specialization" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], biolink:OrganismTaxonToOrganismTaxonAssociation ; skos:definition "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" ; @@ -5802,12 +5802,9 @@ biolink:OrganismToOrganismAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:IndividualOrganism ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], @@ -5816,6 +5813,9 @@ biolink:OrganismToOrganismAssociation a owl:Class ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:IndividualOrganism ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], biolink:Association ; skos:inScheme . @@ -5825,18 +5825,18 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismalEntity ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], biolink:Association ; skos:inScheme . @@ -5844,49 +5844,49 @@ biolink:PairwiseMolecularInteraction a owl:Class ; rdfs:label "pairwise molecular interaction" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:interacting_molecules_category ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:interacting_molecules_category ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:id ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularEntity ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:interacting_molecules_category ], + owl:maxCardinality 1 ; + owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:interacting_molecules_category ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularEntity ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:interacting_molecules_category ], + owl:onProperty biolink:subject ], biolink:PairwiseGeneToGeneInteraction ; skos:definition "An interaction at the molecular level between two physical entities" ; skos:inScheme . @@ -5978,17 +5978,17 @@ biolink:Phenomenon a owl:Class ; biolink:PhenotypicFeatureToDiseaseAssociation a owl:Class ; rdfs:label "phenotypic feature to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], @@ -6049,20 +6049,14 @@ biolink:Plant a owl:Class ; biolink:PopulationToPopulationAssociation a owl:Class ; rdfs:label "population to population association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], @@ -6071,6 +6065,12 @@ biolink:PopulationToPopulationAssociation a owl:Class ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; @@ -6092,193 +6092,193 @@ biolink:PredicateMapping a owl:Class ; rdfs:label "predicate mapping" ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:broad_match ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:exact_match ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:broad_match ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:exact_match ], + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:mapped_predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:exact_match ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:narrow_match ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_derivative_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:exact_match ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_part_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:broad_match ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object_derivative_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:mapped_predicate ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:narrow_match ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:species_context_qualifier ], + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:object_part_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:exact_match ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:mapped_predicate ], + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_derivative_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:narrow_match ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:mapped_predicate ], + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:narrow_match ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:narrow_match ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:mapped_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:broad_match ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_derivative_qualifier ], + owl:onProperty biolink:narrow_match ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:mapped_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:broad_match ], linkml:ClassDefinition ; 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." ; skos:inScheme . @@ -6294,31 +6294,31 @@ biolink:PreprintPublication a owl:Class ; biolink:ProcessRegulatesProcessAssociation a owl:Class ; rdfs:label "process regulates process association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalProcess ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:BiologicalProcess ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalProcess ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:BiologicalProcess ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "Describes a regulatory relationship between two genes or gene products." ; @@ -6335,10 +6335,10 @@ biolink:ProteinDomain a owl:Class ; rdfs:label "protein domain" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneGroupingMixin ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:GeneGroupingMixin ], biolink:BiologicalEntity ; skos:definition "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." ; skos:exactMatch , @@ -6350,10 +6350,10 @@ biolink:ProteinFamily a owl:Class ; rdfs:label "protein family" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneGroupingMixin ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:GeneGroupingMixin ], biolink:BiologicalEntity ; skos:exactMatch , WIKIDATA:Q2278983 ; @@ -6428,14 +6428,14 @@ biolink:ReactionToCatalystAssociation a owl:Class ; biolink:ReagentTargetedGene a owl:Class ; rdfs:label "reagent targeted gene" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhysicalEssence ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GenomicEntity ], biolink:BiologicalEntity ; skos:altLabel "sequence targeting reagent" ; skos:definition "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." ; @@ -6482,23 +6482,23 @@ biolink:SequenceEnum a owl:Class ; biolink:SequenceVariantModulatesTreatmentAssociation a owl:Class ; rdfs:label "sequence variant modulates treatment association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Treatment ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Treatment ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ; skos:inScheme ; @@ -6507,46 +6507,46 @@ biolink:SequenceVariantModulatesTreatmentAssociation a owl:Class ; biolink:Serial a owl:Class ; rdfs:label "serial" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:iso_abbreviation ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:issue ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; + owl:onProperty biolink:type ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:type ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:volume ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:type ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:issue ], + owl:minCardinality 1 ; + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:volume ], + owl:onProperty biolink:issue ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:iso_abbreviation ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:issue ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:type ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:volume ], biolink:Publication ; skos:altLabel "journal" ; @@ -6596,14 +6596,14 @@ biolink:Snv a owl:Class ; biolink:SocioeconomicExposure a owl:Class ; rdfs:label "socioeconomic exposure" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ExposureEvent ], + [ a owl:Restriction ; owl:allValuesFrom biolink:SocioeconomicAttribute ; owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:has_attribute ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ExposureEvent ], biolink:Attribute ; skos:definition "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty)." ; skos:inScheme . @@ -6655,23 +6655,23 @@ biolink:StudyVariable a owl:Class ; biolink:TaxonToTaxonAssociation a owl:Class ; rdfs:label "taxon to taxon association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:object ], biolink:Association ; skos:inScheme . @@ -6691,22 +6691,22 @@ biolink:TextMiningResult a owl:Class ; biolink:TranscriptToGeneRelationship a owl:Class ; rdfs:label "transcript to gene relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Transcript ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Transcript ; owl:onProperty biolink:subject ], biolink:SequenceFeatureRelationship ; skos:definition "A gene is a collection of transcripts" ; @@ -6716,16 +6716,16 @@ biolink:TranscriptionFactorBindingSite a owl:Class ; rdfs:label "transcription factor binding site" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:PhysicalEssence ], biolink:RegulatoryRegion ; skos:altLabel "binding site", "tf binding site" ; @@ -6736,20 +6736,20 @@ biolink:TranscriptionFactorBindingSite a owl:Class ; biolink:VariantAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "variant as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], biolink:VariantToDiseaseAssociation ; skos:inScheme . @@ -6759,13 +6759,13 @@ biolink:VariantToGeneExpressionAssociation a owl:Class ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneExpressionMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], biolink:VariantToGeneAssociation ; skos:definition "An association between a variant and expression of a gene (i.e. e-QTL)" ; @@ -6779,12 +6779,12 @@ biolink:VariantToPhenotypicFeatureAssociation a owl:Class ; [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], @@ -6794,59 +6794,59 @@ biolink:VariantToPhenotypicFeatureAssociation a owl:Class ; biolink:VariantToPopulationAssociation a owl:Class ; rdfs:label "variant to population association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_total ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:FrequencyQualifierMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_quotient ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQuantifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; - owl:onProperty biolink:object ], + owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_count ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_count ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_count ], + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_quotient ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], + owl:someValuesFrom biolink:FrequencyQuantifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_count ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_total ], biolink:Association ; skos:definition "An association between a variant and a population, where the variant has particular frequency in the population" ; skos:inScheme . @@ -7418,41 +7418,41 @@ biolink:AdministrativeEntity a owl:Class ; biolink:Article a owl:Class ; rdfs:label "article" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:issue ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:volume ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:published_in ], + owl:maxCardinality 1 ; + owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:issue ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:volume ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; + owl:maxCardinality 1 ; owl:onProperty biolink:published_in ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:published_in ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:issue ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:volume ], + owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:volume ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:published_in ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:iso_abbreviation ], + owl:onProperty biolink:volume ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:issue ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:iso_abbreviation ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + 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, @@ -7485,8 +7485,11 @@ biolink:BehavioralFeature a owl:Class ; biolink:BookChapter a owl:Class ; rdfs:label "book chapter" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:chapter ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:published_in ], @@ -7494,23 +7497,20 @@ biolink:BookChapter a owl:Class ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:volume ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:volume ], + owl:minCardinality 1 ; + owl:onProperty biolink:published_in ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:chapter ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:published_in ], + owl:onProperty biolink:chapter ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:chapter ], + owl:onProperty biolink:volume ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:published_in ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:volume ], biolink:Publication ; skos:inScheme . @@ -7528,11 +7528,8 @@ biolink:Case a owl:Class ; biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "cell line to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:CellLineToEntityAssociationMixin ], @@ -7540,8 +7537,11 @@ biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "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." ; skos:inScheme . @@ -7561,14 +7561,14 @@ biolink:ChemicalEntityToEntityAssociationMixin a owl:Class ; biolink:ChemicalExposure a owl:Class ; rdfs:label "chemical exposure" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:QuantityValue ; - owl:onProperty biolink:has_quantitative_value ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ExposureEvent ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_quantitative_value ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:QuantityValue ; + owl:onProperty biolink:has_quantitative_value ], biolink:Attribute ; skos:definition "A chemical exposure is an intake of a particular chemical entity." ; skos:exactMatch ECTO:9000000, @@ -7578,14 +7578,14 @@ biolink:ChemicalExposure a owl:Class ; biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "chemical or drug or treatment to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:FDAIDAAdverseEventEnum ; owl:onProperty biolink:FDA_adverse_event_level ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:FDA_adverse_event_level ], @@ -7593,14 +7593,14 @@ biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a owl:C owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:FDAIDAAdverseEventEnum ; + owl:minCardinality 0 ; owl:onProperty biolink:FDA_adverse_event_level ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "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." ; skos:inScheme . @@ -7726,10 +7726,10 @@ biolink:GeneFamily a owl:Class ; rdfs:label "gene family" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneGroupingMixin ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:GeneGroupingMixin ], biolink:BiologicalEntity ; skos:altLabel "orthogroup", "protein family" ; @@ -7745,76 +7745,76 @@ biolink:GenomicSequenceLocalization a owl:Class ; rdfs:label "genomic sequence localization" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:genome_build ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:end_interbase_coordinate ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:phase ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:start_interbase_coordinate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:strand ], [ a owl:Restriction ; owl:allValuesFrom biolink:StrandEnum ; owl:onProperty biolink:strand ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:end_interbase_coordinate ], + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:start_interbase_coordinate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:start_interbase_coordinate ], + owl:onProperty biolink:end_interbase_coordinate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:strand ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:phase ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:strand ], [ a owl:Restriction ; owl:allValuesFrom biolink:PhaseEnum ; owl:onProperty biolink:phase ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:end_interbase_coordinate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:start_interbase_coordinate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:end_interbase_coordinate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NucleicAcidEntity ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:NucleicAcidEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:phase ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:phase ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:start_interbase_coordinate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:genome_build ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:genome_build ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NucleicAcidEntity ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:StrandEnum ; owl:onProperty biolink:genome_build ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:strand ], 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." ; @@ -7824,38 +7824,38 @@ biolink:GenomicSequenceLocalization a owl:Class ; biolink:GenotypeToDiseaseAssociation a owl:Class ; rdfs:label "genotype to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], biolink:Association ; skos:inScheme ; skos:note "TODO decide no how to model pathogenicity" . @@ -7868,7 +7868,7 @@ biolink:GenotypeToEntityAssociationMixin a owl:Class ; biolink:GeographicLocation a owl:Class ; rdfs:label "geographic location" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:float ; owl:onProperty biolink:longitude ], [ a owl:Restriction ; owl:allValuesFrom xsd:float ; @@ -7878,13 +7878,13 @@ biolink:GeographicLocation a owl:Class ; owl:onProperty biolink:latitude ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:longitude ], + owl:onProperty biolink:latitude ], [ a owl:Restriction ; - owl:allValuesFrom xsd:float ; + owl:maxCardinality 1 ; owl:onProperty biolink:longitude ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:latitude ], + owl:minCardinality 0 ; + owl:onProperty biolink:longitude ], biolink:PlanetaryEntity ; skos:definition "a location that can be described in lat/long coordinates" ; skos:exactMatch STY:T083, @@ -7966,41 +7966,41 @@ biolink:Polypeptide a owl:Class ; biolink:ReactionToParticipantAssociation a owl:Class ; rdfs:label "reaction to participant association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:reaction_side ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:reaction_side ], + owl:onProperty biolink:stoichiometry ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:stoichiometry ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:ReactionDirectionEnum ; owl:onProperty biolink:reaction_direction ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:reaction_direction ], [ a owl:Restriction ; owl:allValuesFrom xsd:integer ; owl:onProperty biolink:stoichiometry ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:stoichiometry ], [ a owl:Restriction ; owl:allValuesFrom biolink:ReactionSideEnum ; owl:onProperty biolink:reaction_side ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularEntity ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ReactionDirectionEnum ; + owl:maxCardinality 1 ; owl:onProperty biolink:reaction_direction ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:reaction_side ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:reaction_side ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:stoichiometry ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:ChemicalToChemicalAssociation ; skos:inScheme . @@ -8032,29 +8032,29 @@ biolink:StudyPopulation a owl:Class ; biolink:Treatment a owl:Class ; rdfs:label "treatment" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Drug ; - owl:onProperty biolink:has_drug ], - [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_drug ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ExposureEvent ], + owl:onProperty biolink:has_device ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_procedure ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_drug ], [ a owl:Restriction ; owl:allValuesFrom biolink:Device ; owl:onProperty biolink:has_device ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_device ], + owl:allValuesFrom biolink:Drug ; + owl:onProperty biolink:has_drug ], [ a owl:Restriction ; owl:allValuesFrom biolink:Procedure ; owl:onProperty biolink:has_procedure ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ExposureEvent ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], biolink:NamedThing ; skos:altLabel "medical action", "medical intervention" ; @@ -8067,29 +8067,26 @@ biolink:Treatment a owl:Class ; biolink:VariantToDiseaseAssociation a owl:Class ; rdfs:label "variant to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], @@ -8097,8 +8094,11 @@ biolink:VariantToDiseaseAssociation a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:object ], biolink:Association ; skos:inScheme ; skos:note "TODO decide no how to model pathogenicity" . @@ -8111,15 +8111,15 @@ biolink:VariantToGeneAssociation a owl:Class ; [ a owl:Restriction ; owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], @@ -8783,23 +8783,23 @@ biolink:ActivityAndBehavior a owl:Class ; biolink:AnatomicalEntityToAnatomicalEntityAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:inScheme . @@ -8831,32 +8831,32 @@ biolink:ChemicalRole a owl:Class ; biolink:ChemicalToChemicalAssociation a owl:Class ; rdfs:label "chemical to chemical association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], @@ -8936,56 +8936,56 @@ biolink:FrequencyQualifierMixin a owl:Class ; biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "gene to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:inScheme ; skos:narrowMatch WBVocab:Gene-Phenotype-Association, @@ -9041,25 +9041,25 @@ biolink:Onset a owl:Class ; biolink:OrganismTaxonToOrganismTaxonAssociation a owl:Class ; rdfs:label "organism taxon to organism taxon association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], biolink:Association ; skos:definition "A relationship between two organism taxon nodes" ; @@ -9108,16 +9108,16 @@ biolink:RegulatoryRegion a owl:Class ; rdfs:label "regulatory region" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:PhysicalEssence ], biolink:BiologicalEntity ; skos:altLabel "regulatory element" ; skos:definition "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" ; @@ -9474,23 +9474,23 @@ biolink:DatasetDistribution a owl:Class ; biolink:DatasetSummary a owl:Class ; rdfs:label "dataset summary" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:source_logo ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:source_logo ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:source_web_page ], + owl:onProperty biolink:source_logo ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:source_web_page ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:source_web_page ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:source_logo ], + owl:onProperty biolink:source_web_page ], biolink:InformationContentEntity ; skos:definition "an item that holds summary level information about a dataset." ; skos:inScheme . @@ -9520,20 +9520,20 @@ biolink:GeneToGeneAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], biolink:Association ; skos:altLabel "molecular or genetic interaction" ; skos:definition "abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction." ; @@ -9615,19 +9615,19 @@ biolink:Protein a owl:Class ; biolink:QuantityValue a owl:Class ; rdfs:label "quantity value" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty biolink:has_unit ], + owl:allValuesFrom xsd:double ; + owl:onProperty biolink:has_numeric_value ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_unit ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_numeric_value ], + owl:allValuesFrom ; + owl:onProperty biolink:has_unit ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_numeric_value ], [ a owl:Restriction ; - owl:allValuesFrom xsd:double ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_numeric_value ], [ a owl:Restriction ; owl:minCardinality 0 ; @@ -9646,19 +9646,19 @@ biolink:ResourceRoleEnum a owl:Class ; biolink:SequenceFeatureRelationship a owl:Class ; rdfs:label "sequence feature relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:NucleicAcidEntity ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:NucleicAcidEntity ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:NucleicAcidEntity ; @@ -9783,29 +9783,29 @@ biolink:ClinicalAttribute a owl:Class ; biolink:DatasetVersion a owl:Class ; rdfs:label "dataset version" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:ingest_date ], - [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:has_distribution ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:has_dataset ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DatasetDistribution ; + owl:onProperty biolink:has_distribution ], [ a owl:Restriction ; owl:allValuesFrom biolink:Dataset ; owl:onProperty biolink:has_dataset ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_distribution ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_dataset ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:ingest_date ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_dataset ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DatasetDistribution ; - owl:onProperty biolink:has_distribution ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_distribution ], + owl:onProperty biolink:ingest_date ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:ingest_date ], @@ -9837,22 +9837,22 @@ biolink:FDAIDAAdverseEventEnum a owl:Class ; biolink:FunctionalAssociation a owl:Class ; rdfs:label "functional association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:MacromolecularMachineMixin ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:object ], 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." ; @@ -10240,37 +10240,37 @@ biolink:ChemicalMixture a owl:Class ; rdfs:label "chemical mixture" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:highest_FDA_approval_status ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:drug_regulatory_status_world_wide ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:drug_regulatory_status_world_wide ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:is_supplement ], + owl:onProperty biolink:routes_of_delivery ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ApprovalStatusEnum ; + owl:onProperty biolink:highest_FDA_approval_status ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:is_supplement ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ApprovalStatusEnum ; + owl:maxCardinality 1 ; owl:onProperty biolink:drug_regulatory_status_world_wide ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:highest_FDA_approval_status ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:routes_of_delivery ], + owl:onProperty biolink:is_supplement ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ApprovalStatusEnum ; + owl:onProperty biolink:drug_regulatory_status_world_wide ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:highest_FDA_approval_status ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:is_supplement ], [ a owl:Restriction ; owl:allValuesFrom biolink:DrugDeliveryEnum ; owl:onProperty biolink:routes_of_delivery ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ApprovalStatusEnum ; - 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." ; @@ -10296,28 +10296,28 @@ biolink:GeneProductMixin a owl:Class ; biolink:GeneToDiseaseAssociation a owl:Class ; rdfs:label "gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:Disease ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; skos:closeMatch dcid:DiseaseGeneAssociation ; @@ -10334,38 +10334,38 @@ biolink:MacromolecularMachineMixin a owl:Class ; biolink:MolecularActivity a owl:Class ; rdfs:label "molecular activity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_input ], - [ a owl:Restriction ; owl:allValuesFrom biolink:MacromolecularMachineMixin ; owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularEntity ; + owl:minCardinality 0 ; owl:onProperty biolink:has_output ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:enabled_by ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_input ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:maxCardinality 1 ; + owl:onProperty biolink:has_input ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:Occurrent ], + owl:maxCardinality 1 ; + owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:has_input ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_output ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularEntity ; - owl:onProperty biolink:has_input ], + owl:onProperty biolink:has_output ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_output ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:Occurrent ], biolink:BiologicalProcessOrActivity ; skos:altLabel "molecular event", "molecular function", @@ -10385,35 +10385,35 @@ biolink:PhysicalEssenceOrOccurrent a owl:Class ; biolink:RetrievalSource a owl:Class ; rdfs:label "retrieval source" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:ResourceRoleEnum ; - owl:onProperty biolink:resource_role ], + owl:minCardinality 0 ; + owl:onProperty biolink:upstream_resource_ids ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:ResourceRoleEnum ; owl:onProperty biolink:resource_role ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:resource_id ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:upstream_resource_ids ], + owl:onProperty biolink:resource_role ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:upstream_resource_ids ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:xref ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; + owl:maxCardinality 1 ; owl:onProperty biolink:resource_id ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:upstream_resource_ids ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:resource_id ], + owl:onProperty biolink:upstream_resource_ids ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; + owl:minCardinality 0 ; owl:onProperty biolink:xref ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:resource_id ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:resource_role ], @@ -10760,10 +10760,10 @@ biolink:Drug a owl:Class ; rdfs:label "drug" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], biolink:MolecularMixture ; skos:broadMatch STY:T121 ; skos:definition "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease" ; @@ -10778,23 +10778,23 @@ biolink:Drug a owl:Class ; biolink:Genotype a owl:Class ; rdfs:label "genotype" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Zygosity ; - owl:onProperty biolink:has_zygosity ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:has_zygosity ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:Zygosity ; owl:onProperty biolink:has_zygosity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssence ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_zygosity ], biolink:BiologicalEntity ; skos:definition "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" ; skos:exactMatch , @@ -10888,17 +10888,20 @@ biolink:AgentTypeEnum a owl:Class ; biolink:Entity a owl:Class ; rdfs:label "entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:type ], + owl:maxCardinality 1 ; + owl:onProperty biolink:iri ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Attribute ; + owl:minCardinality 0 ; owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:iri ], + owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:category ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:deprecated ], @@ -10906,50 +10909,47 @@ biolink:Entity a owl:Class ; owl:minCardinality 0 ; owl:onProperty biolink:description ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:category ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], + owl:minCardinality 0 ; + owl:onProperty biolink:iri ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:deprecated ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:category ], + owl:minCardinality 0 ; + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:type ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:iri ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:description ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:description ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:category ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:type ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:Attribute ; owl:onProperty biolink:has_attribute ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:name ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:iri ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:type ], + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:allValuesFrom xsd:boolean ; owl:onProperty biolink:deprecated ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:description ], linkml:ClassDefinition ; skos:definition "Root Biolink Model class for all things and informational relationships, real or imagined." ; skos:inScheme . @@ -11052,14 +11052,14 @@ biolink:NucleicAcidEntity a owl:Class ; biolink:OrganismalEntity a owl:Class ; rdfs:label "organismal entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SubjectOfInvestigation ], + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:has_attribute ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:SubjectOfInvestigation ], biolink:BiologicalEntity ; skos:definition "A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities" ; skos:exactMatch , @@ -11167,38 +11167,38 @@ biolink:GeneOrGeneProductOrChemicalPartQualifierEnum a owl:Class ; biolink:BiologicalProcessOrActivity a owl:Class ; rdfs:label "biological process or activity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_input ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_input ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:has_output ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:allValuesFrom biolink:PhysicalEntity ; + owl:onProperty biolink:enabled_by ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:has_output ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_output ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:Occurrent ], + owl:maxCardinality 1 ; + owl:onProperty biolink:has_input ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:has_input ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_input ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:has_input ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:Occurrent ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:enabled_by ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:PhysicalEntity ; - owl:onProperty biolink:enabled_by ], biolink:BiologicalEntity ; skos:definition "Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system." ; skos:inScheme . @@ -11206,38 +11206,38 @@ biolink:BiologicalProcessOrActivity a owl:Class ; biolink:Agent a owl:Class ; rdfs:label "agent" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:address ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:affiliation ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:address ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:affiliation ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:address ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:address ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:name ], + owl:minCardinality 0 ; + owl:onProperty biolink:affiliation ], biolink:AdministrativeEntity ; skos:altLabel "group" ; skos:definition "person, group, organization or project that provides a piece of information (i.e. a knowledge association)" ; @@ -11353,13 +11353,13 @@ biolink:DirectionQualifierEnum a owl:Class ; biolink:MolecularEntity a owl:Class ; rdfs:label "molecular entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:is_metabolite ], [ a owl:Restriction ; owl:allValuesFrom xsd:boolean ; owl:onProperty biolink:is_metabolite ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:is_metabolite ], biolink:ChemicalEntity ; skos:definition "A molecular entity is a chemical entity composed of individual or covalently bonded atoms." ; @@ -11375,10 +11375,10 @@ biolink:OrganismTaxon a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:has_taxonomic_rank ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:TaxonomicRank ; owl:onProperty biolink:has_taxonomic_rank ], [ a owl:Restriction ; - owl:allValuesFrom biolink:TaxonomicRank ; + owl:minCardinality 0 ; owl:onProperty biolink:has_taxonomic_rank ], biolink:NamedThing ; skos:altLabel "taxon", @@ -11409,41 +11409,41 @@ biolink:BiologicalProcess a owl:Class ; biolink:InformationContentEntity a owl:Class ; rdfs:label "information content entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:format ], + owl:minCardinality 0 ; + owl:onProperty biolink:creation_date ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:license ], + owl:onProperty biolink:creation_date ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:license ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:creation_date ], + owl:maxCardinality 1 ; + owl:onProperty biolink:license ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:rights ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:license ], + owl:onProperty biolink:rights ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:format ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:rights ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:format ], [ a owl:Restriction ; - owl:allValuesFrom xsd:date ; - owl:onProperty biolink:creation_date ], + owl:minCardinality 0 ; + owl:onProperty biolink:format ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:rights ], + owl:onProperty biolink:license ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:date ; owl:onProperty biolink:creation_date ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:rights ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:rights ], biolink:NamedThing ; skos:altLabel "information", "information artefact", @@ -11501,50 +11501,50 @@ biolink:CausalMechanismQualifierEnum a owl:Class ; biolink:Attribute a owl:Class ; rdfs:label "attribute" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:iri ], + [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_quantitative_value ], + owl:onProperty biolink:iri ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_qualitative_value ], + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:has_attribute_type ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:iri ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:has_qualitative_value ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:QuantityValue ; - owl:onProperty biolink:has_quantitative_value ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:has_attribute_type ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_quantitative_value ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:name ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; + owl:minCardinality 1 ; owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:name ], + owl:allValuesFrom biolink:QuantityValue ; + owl:onProperty biolink:has_quantitative_value ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:iri ], + owl:onProperty biolink:has_qualitative_value ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:name ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:iri ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:has_qualitative_value ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:iri ], biolink:NamedThing ; 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." ; skos:exactMatch SIO:000614 ; @@ -11569,35 +11569,35 @@ biolink:object_direction_qualifier a owl:ObjectProperty ; biolink:Gene a owl:Class ; rdfs:label "gene" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:minCardinality 0 ; + owl:onProperty biolink:symbol ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:symbol ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:xref ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:symbol ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneOrGeneProduct ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:xref ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:symbol ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneOrGeneProduct ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:symbol ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssence ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OntologyClass ], biolink:BiologicalEntity ; skos:broadMatch ; skos:definition "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." ; @@ -11611,38 +11611,38 @@ biolink:Gene a owl:Class ; biolink:SequenceVariant a owl:Class ; rdfs:label "sequence variant" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_gene ], + owl:onProperty biolink:has_biological_sequence ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_biological_sequence ], + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:id ], + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:has_gene ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_biological_sequence ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:has_biological_sequence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; + owl:minCardinality 0 ; owl:onProperty biolink:has_gene ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_biological_sequence ], biolink:BiologicalEntity ; skos:altLabel "allele" ; skos:closeMatch , @@ -11686,65 +11686,65 @@ biolink:AnatomicalEntity a owl:Class ; biolink:Publication a owl:Class ; rdfs:label "publication" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:pages ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:summary ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:minCardinality 0 ; + owl:onProperty biolink:pages ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:publication_type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:keywords ], + owl:onProperty biolink:authors ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:xref ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Agent ; - owl:onProperty biolink:authors ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:name ], + owl:maxCardinality 1 ; + owl:onProperty biolink:summary ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:authors ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:summary ], + owl:onProperty biolink:mesh_terms ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:publication_type ], + owl:onProperty biolink:keywords ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:xref ], + owl:minCardinality 1 ; + owl:onProperty biolink:publication_type ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:pages ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:keywords ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:summary ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:name ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:mesh_terms ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:summary ], + owl:onProperty biolink:keywords ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:xref ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Agent ; + owl:onProperty biolink:authors ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:mesh_terms ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:mesh_terms ], + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:id ], @@ -11771,35 +11771,29 @@ biolink:BiologicalEntity a owl:Class ; biolink:ChemicalEntity a owl:Class ; rdfs:label "chemical entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ], + owl:minCardinality 0 ; + owl:onProperty biolink:max_tolerated_dose ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalRole ; - owl:onProperty biolink:has_chemical_role ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], + owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:trade_name ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:trade_name ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:max_tolerated_dose ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DrugAvailabilityEnum ; - owl:onProperty biolink:available_from ], + owl:onProperty biolink:is_toxic ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:boolean ; owl:onProperty biolink:is_toxic ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:is_toxic ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:trade_name ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:max_tolerated_dose ], @@ -11807,11 +11801,14 @@ biolink:ChemicalEntity a owl:Class ; owl:minCardinality 0 ; owl:onProperty biolink:has_chemical_role ], [ a owl:Restriction ; - owl:allValuesFrom xsd:boolean ; - owl:onProperty biolink:is_toxic ], + owl:allValuesFrom biolink:DrugAvailabilityEnum ; + owl:onProperty biolink:available_from ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:allValuesFrom biolink:ChemicalRole ; + owl:onProperty biolink:has_chemical_role ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:max_tolerated_dose ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:available_from ], @@ -11819,8 +11816,11 @@ biolink:ChemicalEntity a owl:Class ; owl:minCardinality 0 ; owl:onProperty biolink:trade_name ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:max_tolerated_dose ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:trade_name ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], biolink:NamedThing ; skos:broadMatch STY:T167 ; skos:definition "A chemical entity is a physical entity that pertains to chemistry or biochemistry." ; @@ -11959,254 +11959,254 @@ biolink:association_slot a owl:DatatypeProperty ; biolink:Association a owl:Class ; rdfs:label "association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:category ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_label_closure ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:original_subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:knowledge_level ], [ a owl:Restriction ; - owl:allValuesFrom biolink:EvidenceType ; - owl:onProperty biolink:has_evidence ], + owl:maxCardinality 1 ; + owl:onProperty biolink:adjusted_p_value ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:retrieval_source_ids ], + owl:onProperty biolink:p_value ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:knowledge_level ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:original_predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:adjusted_p_value ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:subject_category ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:primary_knowledge_source ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:agent_type ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:KnowledgeLevelEnum ; + owl:onProperty biolink:knowledge_level ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualifier ], + owl:onProperty biolink:type ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object_namespace ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:original_predicate ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:aggregator_knowledge_source ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_closure ], + owl:maxCardinality 1 ; + owl:onProperty biolink:p_value ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_namespace ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:negated ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:type ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_category ], + owl:onProperty biolink:qualifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_category ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_label_closure ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:subject_category ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:object_category ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_namespace ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:knowledge_source ], + owl:onProperty biolink:original_subject ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:timepoint ], + owl:onProperty biolink:original_subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_label_closure ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:aggregator_knowledge_source ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:retrieval_source_ids ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:original_object ], + owl:onProperty biolink:object_category ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_closure ], + owl:onProperty biolink:original_predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_namespace ], + owl:onProperty biolink:original_predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_category_closure ], + owl:allValuesFrom biolink:AgentTypeEnum ; + owl:onProperty biolink:agent_type ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:original_object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:category ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:knowledge_level ], + owl:onProperty biolink:negated ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:object_category_closure ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:knowledge_source ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:float ; - owl:onProperty biolink:adjusted_p_value ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:knowledge_source ], + owl:onProperty biolink:object_namespace ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:subject_category ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:agent_type ], + owl:maxCardinality 1 ; + owl:onProperty biolink:knowledge_source ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:primary_knowledge_source ], [ a owl:Restriction ; owl:allValuesFrom biolink:Publication ; owl:onProperty biolink:publications ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:timepoint ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:object_category ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_namespace ], + owl:onProperty biolink:object_closure ], [ a owl:Restriction ; - owl:allValuesFrom xsd:boolean ; - owl:onProperty biolink:negated ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_closure ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:adjusted_p_value ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:qualifiers ], + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:negated ], + owl:minCardinality 0 ; + owl:onProperty biolink:qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:primary_knowledge_source ], + owl:onProperty biolink:subject_category_closure ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:type ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_category_closure ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:primary_knowledge_source ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_label_closure ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:category ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:qualifiers ], + owl:onProperty biolink:subject_category_closure ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_namespace ], + owl:onProperty biolink:original_subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:primary_knowledge_source ], + owl:allValuesFrom xsd:time ; + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_closure ], + owl:onProperty biolink:subject_label_closure ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:object_category_closure ], + owl:maxCardinality 1 ; + owl:onProperty biolink:agent_type ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_label_closure ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:original_object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_category ], + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; - owl:allValuesFrom xsd:float ; - owl:onProperty biolink:p_value ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:original_predicate ], + owl:allValuesFrom biolink:RetrievalSource ; + owl:onProperty biolink:retrieval_source_ids ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:p_value ], + owl:onProperty biolink:type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_category ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:KnowledgeLevelEnum ; - owl:onProperty biolink:knowledge_level ], + owl:minCardinality 0 ; + owl:onProperty biolink:publications ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:EvidenceType ; + owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_evidence ], + owl:onProperty biolink:subject_category ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:aggregator_knowledge_source ], + owl:onProperty biolink:object_label_closure ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:category ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:original_subject ], + owl:onProperty biolink:qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:subject_category_closure ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:publications ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject_namespace ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:original_object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:time ; - owl:onProperty biolink:timepoint ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:knowledge_source ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:boolean ; + owl:onProperty biolink:negated ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:original_subject ], + owl:onProperty biolink:subject_namespace ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:p_value ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_closure ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:adjusted_p_value ], + owl:onProperty biolink:original_object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:agent_type ], + owl:allValuesFrom xsd:float ; + owl:onProperty biolink:p_value ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AgentTypeEnum ; - owl:onProperty biolink:agent_type ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:knowledge_level ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_closure ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_closure ], + owl:minCardinality 0 ; + owl:onProperty biolink:knowledge_source ], [ a owl:Restriction ; - owl:allValuesFrom biolink:RetrievalSource ; - owl:onProperty biolink:retrieval_source_ids ], + owl:maxCardinality 1 ; + owl:onProperty biolink:negated ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_label_closure ], + owl:allValuesFrom xsd:float ; + owl:onProperty biolink:adjusted_p_value ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:qualifiers ], biolink:Entity ; skos:definition "A typed association between two entities, supported by evidence" ; skos:exactMatch OBAN:association, @@ -12226,38 +12226,38 @@ biolink:related_to_at_instance_level a owl:DatatypeProperty, biolink:NamedThing a owl:Class ; rdfs:label "named thing" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:category ], - [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:synonym ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:synonym ], + owl:minCardinality 1 ; + owl:onProperty biolink:category ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:provided_by ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:xref ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:provided_by ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:full_name ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:category ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:full_name ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:xref ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:xref ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:synonym ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:full_name ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:provided_by ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:category ], biolink:Entity ; skos:definition "a databased entity or concept/class" ; skos:exactMatch STY:T071, @@ -12310,64 +12310,44 @@ biolink:subject a owl:ObjectProperty ; skos:inScheme . [] a owl:Restriction ; - rdfs:subClassOf biolink:MicroRNA ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MicroRNA . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ReagentTargetedGene ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ReagentTargetedGene . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Polypeptide ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Polypeptide . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Zygosity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Zygosity . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ProteinDomain ; + rdfs:subClassOf biolink:BehaviorToBehavioralFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProteinDomain . + owl:someValuesFrom biolink:BehaviorToBehavioralFeatureAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:has_gene_or_gene_product ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_biological_sequence ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_gene_or_gene_product ] ; + owl:onProperty biolink:has_biological_sequence ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneGroupingMixin . + owl:someValuesFrom biolink:EpigenomicEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalExposure ; + rdfs:subClassOf biolink:Snv ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalExposure . + owl:someValuesFrom biolink:Snv . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], @@ -12376,83 +12356,132 @@ biolink:subject a owl:ObjectProperty ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ] ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeature . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:Agent ; + rdfs:subClassOf biolink:PhysicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Agent . + owl:someValuesFrom biolink:PhysicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:LogOddsAnalysisResult ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:LogOddsAnalysisResult . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneProductIsoformMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntityAssessesNamedThingAssociation ; + rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntityAssessesNamedThingAssociation . + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Onset ; + rdfs:subClassOf biolink:DrugToGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Onset . + owl:someValuesFrom biolink:DrugToGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneHomologyAssociation ; + rdfs:subClassOf biolink:Case ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneHomologyAssociation . + owl:someValuesFrom biolink:Case . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalAttribute ; + rdfs:subClassOf biolink:JournalArticle ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalAttribute . + owl:someValuesFrom biolink:JournalArticle . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:Drug ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:Drug . [] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalFeature ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalFeature . + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:PopulationOfIndividualOrganisms ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PopulationOfIndividualOrganisms . + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:name ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:MacromolecularMachineMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:NucleicAcidEntity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NucleicAcidEntity . + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:in_taxon_label ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:in_taxon ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:in_taxon ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:in_taxon_label ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:in_taxon_label ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:in_taxon ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ThingWithTaxon . [] a owl:Restriction ; - rdfs:subClassOf biolink:JournalArticle ; + rdfs:subClassOf biolink:ClinicalCourse ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:JournalArticle . + owl:someValuesFrom biolink:ClinicalCourse . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PathognomonicityQuantifier . + rdfs:subClassOf biolink:TranscriptionFactorBindingSite ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:TranscriptionFactorBindingSite . [] a owl:Restriction ; - rdfs:subClassOf biolink:ExonToTranscriptRelationship ; + rdfs:subClassOf biolink:DruggableGeneToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ExonToTranscriptRelationship . + owl:someValuesFrom biolink:DruggableGeneToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalFinding ; + rdfs:subClassOf biolink:Exon ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalFinding . + owl:someValuesFrom biolink:Exon . [] a owl:Restriction ; rdfs:subClassOf biolink:PosttranslationalModification ; @@ -12460,309 +12489,265 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:PosttranslationalModification . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypicSex ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:Occurrent . + +[] a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ActivityAndBehavior . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ContributorAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypicSex . + owl:someValuesFrom biolink:ContributorAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Attribute ; + rdfs:subClassOf biolink:ChemicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Attribute . + owl:someValuesFrom biolink:ChemicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:ProcessedMaterial ; + rdfs:subClassOf biolink:GeneFamily ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProcessedMaterial . + owl:someValuesFrom biolink:GeneFamily . [] a owl:Restriction ; - rdfs:subClassOf biolink:IndividualOrganism ; + rdfs:subClassOf biolink:NucleosomeModification ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:IndividualOrganism . + owl:someValuesFrom biolink:NucleosomeModification . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToExpressionSiteAssociation ; + rdfs:subClassOf biolink:DatasetSummary ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToExpressionSiteAssociation . + owl:someValuesFrom biolink:DatasetSummary . [] a owl:Restriction ; - rdfs:subClassOf biolink:TranscriptToGeneRelationship ; + rdfs:subClassOf biolink:GenotypeToGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TranscriptToGeneRelationship . + owl:someValuesFrom biolink:GenotypeToGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Bacterium ; + rdfs:subClassOf biolink:CellularComponent ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Bacterium . + owl:someValuesFrom biolink:CellularComponent . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalEntity ; + rdfs:subClassOf biolink:MaterialSample ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalEntity . + owl:someValuesFrom biolink:MaterialSample . [] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityAssociation ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityAssociation . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeature . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalAnatomicalStructure ; + rdfs:subClassOf biolink:EnvironmentalExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalAnatomicalStructure . + owl:someValuesFrom biolink:EnvironmentalExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellularComponent ; + rdfs:subClassOf biolink:WebPage ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellularComponent . + owl:someValuesFrom biolink:WebPage . [] a owl:Restriction ; - rdfs:subClassOf biolink:NucleicAcidSequenceMotif ; + rdfs:subClassOf biolink:EnvironmentalFoodContaminant ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NucleicAcidSequenceMotif . + owl:someValuesFrom biolink:EnvironmentalFoodContaminant . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:MicroRNA ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:MicroRNA . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:EntityToDiseaseAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:EntityToDiseaseAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:OrganismAttribute ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:OrganismAttribute . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:PhenotypicFeature ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ] ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin . + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivityToMolecularActivityAssociation ; + rdfs:subClassOf biolink:Association ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivityToMolecularActivityAssociation . + owl:someValuesFrom biolink:Association . [] a owl:Restriction ; - rdfs:subClassOf biolink:WebPage ; + rdfs:subClassOf biolink:AccessibleDnaRegion ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:WebPage . + owl:someValuesFrom biolink:AccessibleDnaRegion . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:SequenceFeatureRelationship ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:SequenceFeatureRelationship . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:RNAProduct ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:RNAProduct . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:ExposureEvent ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MaterialSample ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ] ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MaterialSampleToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Association ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Association . + owl:someValuesFrom biolink:EntityToExposureEventAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntity ; + rdfs:subClassOf biolink:GeographicExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntity . + owl:someValuesFrom biolink:GeographicExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:Invertebrate ; + rdfs:subClassOf biolink:ProcessedMaterial ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Invertebrate . + owl:someValuesFrom biolink:ProcessedMaterial . [] a owl:Restriction ; - rdfs:subClassOf biolink:SocioeconomicAttribute ; + rdfs:subClassOf biolink:TextMiningResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SocioeconomicAttribute . + owl:someValuesFrom biolink:TextMiningResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:TranscriptionFactorBindingSite ; + rdfs:subClassOf biolink:DatasetVersion ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TranscriptionFactorBindingSite . + owl:someValuesFrom biolink:DatasetVersion . [] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalSex ; + rdfs:subClassOf biolink:ReagentTargetedGene ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalSex . + owl:someValuesFrom biolink:ReagentTargetedGene . [] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularMachineToCellularComponentAssociation ; + rdfs:subClassOf biolink:Attribute ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularMachineToCellularComponentAssociation . + owl:someValuesFrom biolink:Attribute . [] a owl:Restriction ; - rdfs:subClassOf biolink:SiRNA ; + rdfs:subClassOf biolink:GeneToGeneHomologyAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SiRNA . + owl:someValuesFrom biolink:GeneToGeneHomologyAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivityToChemicalEntityAssociation ; + rdfs:subClassOf biolink:PhenotypicFeature ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivityToChemicalEntityAssociation . + owl:someValuesFrom biolink:PhenotypicFeature . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureExposure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureExposure . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceVariantModulatesTreatmentAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceVariantModulatesTreatmentAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:EvidenceType ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EvidenceType . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Gene ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Gene . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GenomicBackgroundExposure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenomicBackgroundExposure . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeneRegulatesGeneAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneRegulatesGeneAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeneAffectsChemicalAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneAffectsChemicalAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularMachineToBiologicalProcessAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularMachineToBiologicalProcessAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularMixture ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularMixture . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GenomicSequenceLocalization ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenomicSequenceLocalization . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicSex ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicSex . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicFeatureToDiseaseAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicFeatureToDiseaseAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ObservedExpectedFrequencyAnalysisResult ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ObservedExpectedFrequencyAnalysisResult . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:SmallMolecule ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SmallMolecule . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Mammal ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Mammal . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:InformationContentEntityToNamedThingAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:InformationContentEntityToNamedThingAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Haplotype ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Haplotype . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:TextMiningResult ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TextMiningResult . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToGeneAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToGeneAssociation . + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneToEntityAssociationMixin . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:DirectionQualifierEnum ; owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; @@ -12770,570 +12755,555 @@ biolink:subject a owl:ObjectProperty ; [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:DirectionQualifierEnum ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_aspect_qualifier ] ; + owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ] ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:FeatureOrDiseaseQualifiersToEntityMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:RegulatoryRegion ; + rdfs:subClassOf biolink:VariantToGeneExpressionAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RegulatoryRegion . + owl:someValuesFrom biolink:VariantToGeneExpressionAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:MaterialSampleDerivationAssociation ; + rdfs:subClassOf biolink:GeographicLocation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MaterialSampleDerivationAssociation . + owl:someValuesFrom biolink:GeographicLocation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Disease ; + rdfs:subClassOf biolink:Protein ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Disease . + owl:someValuesFrom biolink:Protein . [] a owl:Restriction ; - rdfs:subClassOf biolink:Study ; + rdfs:subClassOf biolink:MacromolecularMachineToMolecularActivityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Study . + owl:someValuesFrom biolink:MacromolecularMachineToMolecularActivityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:RNAProduct ; + rdfs:subClassOf biolink:Haplotype ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RNAProduct . + owl:someValuesFrom biolink:Haplotype . [] a owl:Restriction ; - rdfs:subClassOf biolink:PreprintPublication ; + rdfs:subClassOf biolink:OrganismToOrganismAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PreprintPublication . + owl:someValuesFrom biolink:OrganismToOrganismAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneRegulatesGeneAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneRegulatesGeneAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Book ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Book . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GenotypeToDiseaseAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GenotypeToDiseaseAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:double ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_total ], + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_quotient ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_total ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; - owl:onProperty biolink:has_total ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; - owl:onProperty biolink:has_count ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_count ], + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_percentage ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_count ], + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_percentage ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:double ; - owl:onProperty biolink:has_percentage ] ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty biolink:frequency_qualifier ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQuantifier . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ConfidenceLevel ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ConfidenceLevel . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Procedure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Procedure . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalProcess ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalProcess . + owl:someValuesFrom biolink:FrequencyQualifierMixin . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:has_biological_sequence ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:id ], + owl:onProperty biolink:has_biological_sequence ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ] ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_biological_sequence ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass . + owl:someValuesFrom biolink:GenomicEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:DatasetVersion ; + rdfs:subClassOf biolink:CommonDataElement ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DatasetVersion . + owl:someValuesFrom biolink:CommonDataElement . [] a owl:Restriction ; - rdfs:subClassOf biolink:NamedThing ; + rdfs:subClassOf biolink:GeneHasVariantThatContributesToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NamedThing . + owl:someValuesFrom biolink:GeneHasVariantThatContributesToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalFoodContaminant ; + rdfs:subClassOf biolink:GeneAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalFoodContaminant . + owl:someValuesFrom biolink:GeneAsAModelOfDiseaseAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Event ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Event . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Drug ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ] ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DrugToEntityAssociationMixin . + owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SubjectOfInvestigation . + rdfs:subClassOf biolink:RNAProductIsoform ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:RNAProductIsoform . [] a owl:Restriction ; - rdfs:subClassOf biolink:Hospitalization ; + rdfs:subClassOf biolink:Virus ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Hospitalization . + owl:someValuesFrom biolink:Virus . [] a owl:Restriction ; - rdfs:subClassOf biolink:BehavioralExposure ; + rdfs:subClassOf biolink:TaxonToTaxonAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BehavioralExposure . + owl:someValuesFrom biolink:TaxonToTaxonAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:CellularOrganism ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:CellularOrganism . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:StudyPopulation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:StudyPopulation . [] a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneOrGeneProduct . + owl:someValuesFrom biolink:Outcome . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellLineAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:CellLine ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellLineAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:CellLine . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneFamily ; + rdfs:subClassOf biolink:IndividualOrganism ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneFamily . + owl:someValuesFrom biolink:IndividualOrganism . [] a owl:Restriction ; - rdfs:subClassOf biolink:DrugToGeneInteractionExposure ; + rdfs:subClassOf biolink:ReactionToParticipantAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugToGeneInteractionExposure . + owl:someValuesFrom biolink:ReactionToParticipantAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:InformationContentEntity ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PathognomonicityQuantifier . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:MolecularActivityToChemicalEntityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:InformationContentEntity . + owl:someValuesFrom biolink:MolecularActivityToChemicalEntityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Dataset ; + rdfs:subClassOf biolink:Transcript ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Dataset . + owl:someValuesFrom biolink:Transcript . [] a owl:Restriction ; - rdfs:subClassOf biolink:Plant ; + rdfs:subClassOf biolink:GeneToGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Plant . + owl:someValuesFrom biolink:GeneToGeneAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:has_gene_or_gene_product ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ] ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_gene_or_gene_product ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin . + owl:someValuesFrom biolink:GeneGroupingMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:StudyPopulation ; + rdfs:subClassOf biolink:CodingSequence ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:StudyPopulation . + owl:someValuesFrom biolink:CodingSequence . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonAssociation . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:SubjectOfInvestigation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Serial ; + rdfs:subClassOf biolink:Patent ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Serial . + owl:someValuesFrom biolink:Patent . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGoTermAssociation ; + rdfs:subClassOf biolink:Phenomenon ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGoTermAssociation . + owl:someValuesFrom biolink:Phenomenon . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonSpecialization ; + rdfs:subClassOf biolink:ComplexMolecularMixture ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonSpecialization . + owl:someValuesFrom biolink:ComplexMolecularMixture . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalRole ; + rdfs:subClassOf biolink:PopulationToPopulationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalRole . + owl:someValuesFrom biolink:PopulationToPopulationAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ProcessRegulatesProcessAssociation ; + rdfs:subClassOf biolink:ChemicalExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProcessRegulatesProcessAssociation . + owl:someValuesFrom biolink:ChemicalExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismAttribute ; + rdfs:subClassOf biolink:Human ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismAttribute . + owl:someValuesFrom biolink:Human . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalGeneInteractionAssociation ; + rdfs:subClassOf biolink:PathologicalProcess ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalGeneInteractionAssociation . + owl:someValuesFrom biolink:PathologicalProcess . [] a owl:Restriction ; - rdfs:subClassOf biolink:RetrievalSource ; + rdfs:subClassOf biolink:GenotypeToVariantAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RetrievalSource . + owl:someValuesFrom biolink:GenotypeToVariantAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Virus ; + rdfs:subClassOf biolink:CaseToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Virus . + owl:someValuesFrom biolink:CaseToPhenotypicFeatureAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalEntityToEntityAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneToPathwayAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneToPathwayAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ] ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin . + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalModifier ; + rdfs:subClassOf biolink:Procedure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalModifier . + owl:someValuesFrom biolink:Procedure . [] a owl:Restriction ; - rdfs:subClassOf biolink:EntityToDiseaseAssociation ; + rdfs:subClassOf biolink:SequenceVariantModulatesTreatmentAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EntityToDiseaseAssociation . + owl:someValuesFrom biolink:SequenceVariantModulatesTreatmentAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalAffectsGeneAssociation ; + rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonInteraction ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalAffectsGeneAssociation . + owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonInteraction . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToPathwayAssociation ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToPathwayAssociation . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxon ; + rdfs:subClassOf biolink:AdministrativeEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxon . + owl:someValuesFrom biolink:AdministrativeEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:ContributorAssociation ; + rdfs:subClassOf biolink:MolecularActivityToPathwayAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ContributorAssociation . + owl:someValuesFrom biolink:MolecularActivityToPathwayAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:BehavioralFeature ; + rdfs:subClassOf biolink:LogOddsAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BehavioralFeature . + owl:someValuesFrom biolink:LogOddsAnalysisResult . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:sex_qualifier ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PhenotypicFeature ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:NucleosomeModification ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NucleosomeModification . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:name ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineMixin . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:Occurrent . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:CellLine ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellLine . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeneAsAModelOfDiseaseAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneAsAModelOfDiseaseAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:RelativeFrequencyAnalysisResult ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RelativeFrequencyAnalysisResult . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:BookChapter ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BookChapter . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalProcess ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalProcess . + owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:ObservedExpectedFrequencyAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:ObservedExpectedFrequencyAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:EntityToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:MacromolecularMachineToCellularComponentAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:MacromolecularMachineToCellularComponentAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneHasVariantThatContributesToDiseaseAssociation ; + rdfs:subClassOf biolink:GeneToExpressionSiteAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneHasVariantThatContributesToDiseaseAssociation . + owl:someValuesFrom biolink:GeneToExpressionSiteAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToLocationAssociation ; + rdfs:subClassOf biolink:Pathway ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . + owl:someValuesFrom biolink:Pathway . [] a owl:Restriction ; - rdfs:subClassOf biolink:Article ; + rdfs:subClassOf biolink:VariantAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Article . + owl:someValuesFrom biolink:VariantAsAModelOfDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToPopulationAssociation ; + rdfs:subClassOf biolink:OrganismTaxon ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToPopulationAssociation . + owl:someValuesFrom biolink:OrganismTaxon . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicFeatureToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:ProteinDomain ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicFeatureToPhenotypicFeatureAssociation . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment . + owl:someValuesFrom biolink:ProteinDomain . [] a owl:Restriction ; - rdfs:subClassOf biolink:Activity ; + rdfs:subClassOf biolink:BioticExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Activity . + owl:someValuesFrom biolink:BioticExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:Treatment ; + rdfs:subClassOf biolink:Agent ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Treatment . + owl:someValuesFrom biolink:Agent . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Outcome ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ] ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToOutcomeAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalAnatomicalExposure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalAnatomicalExposure . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . + owl:someValuesFrom biolink:EntityToFeatureOrDiseaseQualifiersMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:NucleicAcidSequenceMotif ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:NucleicAcidSequenceMotif . [] a owl:Restriction ; - rdfs:subClassOf biolink:PairwiseGeneToGeneInteraction ; + rdfs:subClassOf biolink:NucleicAcidEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PairwiseGeneToGeneInteraction . + owl:someValuesFrom biolink:NucleicAcidEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:LifeStage ; + rdfs:subClassOf biolink:ExonToTranscriptRelationship ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:LifeStage . + owl:someValuesFrom biolink:ExonToTranscriptRelationship . [] a owl:Restriction ; - rdfs:subClassOf biolink:Event ; + rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Event . + owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityAssociation . [] a owl:Restriction ; rdfs:subClassOf biolink:Entity ; @@ -13341,138 +13311,120 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:Entity . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivity . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssenceOrOccurrent . [] a owl:Restriction ; - rdfs:subClassOf biolink:SocioeconomicExposure ; + rdfs:subClassOf biolink:BiologicalProcessOrActivity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SocioeconomicExposure . + owl:someValuesFrom biolink:BiologicalProcessOrActivity . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalTrial ; + rdfs:subClassOf biolink:GrossAnatomicalStructure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalTrial . + owl:someValuesFrom biolink:GrossAnatomicalStructure . [] a owl:Restriction ; - rdfs:subClassOf biolink:RNAProductIsoform ; + rdfs:subClassOf biolink:PathologicalAnatomicalStructure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RNAProductIsoform . + owl:someValuesFrom biolink:PathologicalAnatomicalStructure . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:BookChapter ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:BookChapter . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation ; + rdfs:subClassOf biolink:ConceptCountAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . + owl:someValuesFrom biolink:ConceptCountAnalysisResult . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence . + rdfs:subClassOf biolink:NoncodingRNAProduct ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:NoncodingRNAProduct . [] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalEntity ; + rdfs:subClassOf biolink:ProteinFamily ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalEntity . + owl:someValuesFrom biolink:ProteinFamily . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneticInheritance ; + rdfs:subClassOf biolink:GenotypeToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneticInheritance . + owl:someValuesFrom biolink:GenotypeToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Food ; + rdfs:subClassOf biolink:GeneToGeneCoexpressionAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Food . + owl:someValuesFrom biolink:GeneToGeneCoexpressionAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneProductRelationship ; + rdfs:subClassOf biolink:ProcessRegulatesProcessAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneProductRelationship . + owl:someValuesFrom biolink:ProcessRegulatesProcessAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:Drug ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:frequency_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:frequency_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQualifierMixin . + owl:someValuesFrom biolink:DrugToEntityAssociationMixin . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:expression_site ], - [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:expression_site ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:stage_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:phenotypic_state ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:quantifier_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:expression_site ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:quantifier_qualifier ], + owl:allValuesFrom biolink:CellLine ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:phenotypic_state ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:phenotypic_state ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:stage_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:quantifier_qualifier ] ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneExpressionMixin . + owl:someValuesFrom biolink:CellLineToEntityAssociationMixin . [] a owl:Restriction ; rdfs:subClassOf biolink:StudyVariable ; @@ -13480,1017 +13432,1009 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:StudyVariable . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhysicalEntity ; + rdfs:subClassOf biolink:Treatment ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhysicalEntity . + owl:someValuesFrom biolink:Treatment . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularEntity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularEntity . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment . [] a owl:Restriction ; - rdfs:subClassOf biolink:Cohort ; + rdfs:subClassOf biolink:Publication ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Cohort . + owl:someValuesFrom biolink:Publication . [] a owl:Restriction ; - rdfs:subClassOf biolink:Book ; + rdfs:subClassOf biolink:OrganismalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Book . + owl:someValuesFrom biolink:OrganismalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:Genotype ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:Genotype . [] a owl:Restriction ; - rdfs:subClassOf biolink:PlanetaryEntity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PlanetaryEntity . + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:id ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OntologyClass . [] a owl:Restriction ; - rdfs:subClassOf biolink:Publication ; + rdfs:subClassOf biolink:OrganismalEntityAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Publication . + owl:someValuesFrom biolink:OrganismalEntityAsAModelOfDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToDiseaseAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToDiseaseAssociation . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssence . [] a owl:Restriction ; - rdfs:subClassOf biolink:Genome ; + rdfs:subClassOf biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Genome . + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Cell ; + rdfs:subClassOf biolink:ChemicalEntityAssessesNamedThingAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Cell . + owl:someValuesFrom biolink:ChemicalEntityAssessesNamedThingAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:VariantToPopulationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeAsAModelOfDiseaseAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin . + owl:someValuesFrom biolink:VariantToPopulationAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:CaseToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:GenomicSequenceLocalization ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CaseToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:GenomicSequenceLocalization . [] a owl:Restriction ; - rdfs:subClassOf biolink:NoncodingRNAProduct ; + rdfs:subClassOf biolink:Study ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NoncodingRNAProduct . + owl:someValuesFrom biolink:Study . [] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularComplex ; + rdfs:subClassOf biolink:RegulatoryRegion ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularComplex . + owl:someValuesFrom biolink:RegulatoryRegion . [] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalProcessOrActivity ; + rdfs:subClassOf biolink:ReactionToCatalystAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalProcessOrActivity . + owl:someValuesFrom biolink:ReactionToCatalystAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalToPathwayAssociation ; + rdfs:subClassOf biolink:ChemicalMixture ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalToPathwayAssociation . + owl:someValuesFrom biolink:ChemicalMixture . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SensitivityQuantifier . + rdfs:subClassOf biolink:ClinicalIntervention ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ClinicalIntervention . [] a owl:Restriction ; - rdfs:subClassOf biolink:PopulationToPopulationAssociation ; + rdfs:subClassOf biolink:GenotypeToGenotypePartAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PopulationToPopulationAssociation . + owl:someValuesFrom biolink:GenotypeToGenotypePartAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToDiseaseAssociation ; + rdfs:subClassOf biolink:PhysiologicalProcess ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToDiseaseAssociation . + owl:someValuesFrom biolink:PhysiologicalProcess . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalProcessExposure ; + rdfs:subClassOf biolink:GenotypicSex ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalProcessExposure . + owl:someValuesFrom biolink:GenotypicSex . [] a owl:Restriction ; - rdfs:subClassOf biolink:Transcript ; + rdfs:subClassOf biolink:PhenotypicSex ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Transcript . + owl:someValuesFrom biolink:PhenotypicSex . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_biological_sequence ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_biological_sequence ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_biological_sequence ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EpigenomicEntity . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:object ] ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin . + owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:TaxonToTaxonAssociation ; + rdfs:subClassOf biolink:Vertebrate ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TaxonToTaxonAssociation . + owl:someValuesFrom biolink:Vertebrate . [] a owl:Restriction ; - rdfs:subClassOf biolink:StudyResult ; + rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonSpecialization ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:StudyResult . + owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonSpecialization . [] a owl:Restriction ; - rdfs:subClassOf biolink:FunctionalAssociation ; + rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:FunctionalAssociation . + owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:in_taxon_label ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:in_taxon ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:in_taxon ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:in_taxon_label ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:in_taxon_label ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:in_taxon ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ThingWithTaxon . + rdfs:subClassOf biolink:Dataset ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Dataset . [] a owl:Restriction ; - rdfs:subClassOf biolink:ProteinIsoform ; + rdfs:subClassOf biolink:GeographicLocationAtTime ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProteinIsoform . + owl:someValuesFrom biolink:GeographicLocationAtTime . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToGenotypePartAssociation ; + rdfs:subClassOf biolink:Plant ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToGenotypePartAssociation . + owl:someValuesFrom biolink:Plant . [] a owl:Restriction ; - rdfs:subClassOf biolink:SeverityValue ; + rdfs:subClassOf biolink:DiseaseToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SeverityValue . + owl:someValuesFrom biolink:DiseaseToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:CommonDataElement ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CommonDataElement . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Exon ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Exon . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Device ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Device . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalToChemicalAssociation ; + rdfs:subClassOf biolink:Onset ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalToChemicalAssociation . + owl:someValuesFrom biolink:Onset . [] a owl:Restriction ; - rdfs:subClassOf biolink:Snv ; + rdfs:subClassOf biolink:EvidenceType ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Snv . + owl:someValuesFrom biolink:EvidenceType . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:VariantToGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:VariantToGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalMixture ; + rdfs:subClassOf biolink:EnvironmentalFeature ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalMixture . + owl:someValuesFrom biolink:EnvironmentalFeature . [] a owl:Restriction ; - rdfs:subClassOf biolink:DatasetSummary ; + rdfs:subClassOf biolink:ClinicalModifier ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DatasetSummary . + owl:someValuesFrom biolink:ClinicalModifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismalEntity ; + rdfs:subClassOf biolink:PairwiseGeneToGeneInteraction ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismalEntity . + owl:someValuesFrom biolink:PairwiseGeneToGeneInteraction . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToGeneAssociation ; + rdfs:subClassOf biolink:DatasetDistribution ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToGeneAssociation . + owl:someValuesFrom biolink:DatasetDistribution . [] a owl:Restriction ; - rdfs:subClassOf biolink:ConceptCountAnalysisResult ; + rdfs:subClassOf biolink:Zygosity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ConceptCountAnalysisResult . + owl:someValuesFrom biolink:Zygosity . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalProcess ; + rdfs:subClassOf biolink:GeneToGeneFamilyAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalProcess . + owl:someValuesFrom biolink:GeneToGeneFamilyAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalExposure ; + rdfs:subClassOf biolink:MacromolecularComplex ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalExposure . + owl:someValuesFrom biolink:MacromolecularComplex . [] a owl:Restriction ; - rdfs:subClassOf biolink:Pathway ; + rdfs:subClassOf biolink:DrugToGeneInteractionExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Pathway . + owl:someValuesFrom biolink:DrugToGeneInteractionExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceVariant ; + rdfs:subClassOf biolink:ClinicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceVariant . + owl:someValuesFrom biolink:ClinicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicQuality ; + rdfs:subClassOf biolink:ChemicalToPathwayAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicQuality . + owl:someValuesFrom biolink:ChemicalToPathwayAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DrugExposure ; + rdfs:subClassOf biolink:PopulationOfIndividualOrganisms ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugExposure . + owl:someValuesFrom biolink:PopulationOfIndividualOrganisms . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:time ; - owl:onProperty biolink:timepoint ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:timepoint ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:timepoint ] ; + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ExposureEvent . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Fungus ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Fungus . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToPhenotypicFeatureAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToPhenotypicFeatureAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Vertebrate ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Vertebrate . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneCoexpressionAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneCoexpressionAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToVariantAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToVariantAssociation . + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntity ; + rdfs:subClassOf biolink:InformationContentEntityToNamedThingAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntity . + owl:someValuesFrom biolink:InformationContentEntityToNamedThingAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; - owl:allValuesFrom biolink:CellLine ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_total ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom xsd:integer ; + owl:onProperty biolink:has_total ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:integer ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ] ; + owl:onProperty biolink:has_total ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:double ; + owl:onProperty biolink:has_percentage ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_percentage ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:double ; + owl:onProperty biolink:has_quotient ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:CellLineToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ComplexChemicalExposure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ComplexChemicalExposure . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivityToPathwayAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivityToPathwayAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneFamilyAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneFamilyAssociation . + owl:someValuesFrom biolink:FrequencyQuantifier . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:MaterialSample ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Case ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:CaseToEntityAssociationMixin . + owl:someValuesFrom biolink:MaterialSampleToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ExposureEventToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:SocioeconomicAttribute ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ExposureEventToPhenotypicFeatureAssociation . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssenceOrOccurrent . + owl:someValuesFrom biolink:SocioeconomicAttribute . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:PhenotypicFeature ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ] ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:sex_qualifier ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin . + owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiagnosticAid ; + rdfs:subClassOf biolink:GeneToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiagnosticAid . + owl:someValuesFrom biolink:GeneToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ReactionToParticipantAssociation ; + rdfs:subClassOf biolink:Cohort ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ReactionToParticipantAssociation . + owl:someValuesFrom biolink:Cohort . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeographicLocationAtTime ; + rdfs:subClassOf biolink:Food ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeographicLocationAtTime . + owl:someValuesFrom biolink:Food . [] a owl:Restriction ; - rdfs:subClassOf biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation ; + rdfs:subClassOf biolink:BiologicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . + owl:someValuesFrom biolink:BiologicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:BehaviorToBehavioralFeatureAssociation ; + rdfs:subClassOf biolink:ProteinIsoform ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BehaviorToBehavioralFeatureAssociation . + owl:someValuesFrom biolink:ProteinIsoform . [] a owl:Restriction ; - rdfs:subClassOf biolink:AccessibleDnaRegion ; + rdfs:subClassOf biolink:Invertebrate ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AccessibleDnaRegion . + owl:someValuesFrom biolink:Invertebrate . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseToExposureEventAssociation ; + rdfs:subClassOf biolink:PathologicalProcessExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseToExposureEventAssociation . + owl:someValuesFrom biolink:PathologicalProcessExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:ComplexMolecularMixture ; + rdfs:subClassOf biolink:FunctionalAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ComplexMolecularMixture . + owl:someValuesFrom biolink:FunctionalAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismToOrganismAssociation ; + rdfs:subClassOf biolink:ChemicalRole ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismToOrganismAssociation . + owl:someValuesFrom biolink:ChemicalRole . [] a owl:Restriction ; - rdfs:subClassOf biolink:DatasetDistribution ; + rdfs:subClassOf biolink:GenotypeAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DatasetDistribution . + owl:someValuesFrom biolink:GenotypeAsAModelOfDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalIntervention ; + rdfs:subClassOf biolink:Mammal ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalIntervention . + owl:someValuesFrom biolink:Mammal . [] a owl:Restriction ; - rdfs:subClassOf biolink:Protein ; + rdfs:subClassOf biolink:ClinicalFinding ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Protein . + owl:someValuesFrom biolink:ClinicalFinding . [] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularMachineToMolecularActivityAssociation ; + rdfs:subClassOf biolink:PhenotypicFeatureToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularMachineToMolecularActivityAssociation . + owl:someValuesFrom biolink:PhenotypicFeatureToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Genotype ; + rdfs:subClassOf biolink:MolecularActivity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Genotype . + owl:someValuesFrom biolink:MolecularActivity . [] a owl:Restriction ; - rdfs:subClassOf biolink:FoodAdditive ; + rdfs:subClassOf biolink:VariantToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:FoodAdditive . + owl:someValuesFrom biolink:VariantToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToDiseaseAssociation ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:SmallMolecule ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToDiseaseAssociation . + owl:someValuesFrom biolink:SmallMolecule . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:synonym ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:xref ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:xref ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:synonym ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneProductMixin . + owl:someValuesFrom biolink:RelationshipQuantifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneAssociation ; + rdfs:subClassOf biolink:TranscriptToGeneRelationship ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneAssociation . + owl:someValuesFrom biolink:TranscriptToGeneRelationship . [] a owl:Restriction ; - rdfs:subClassOf biolink:Phenomenon ; + rdfs:subClassOf biolink:Hospitalization ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Phenomenon . + owl:someValuesFrom biolink:Hospitalization . [] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceFeatureRelationship ; + rdfs:subClassOf biolink:OrganismTaxonToEnvironmentAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceFeatureRelationship . + owl:someValuesFrom biolink:OrganismTaxonToEnvironmentAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ExposureEventToOutcomeAssociation ; + rdfs:subClassOf biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ExposureEventToOutcomeAssociation . + owl:someValuesFrom biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhysiologicalProcess ; + rdfs:subClassOf biolink:PhenotypicQuality ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhysiologicalProcess . + owl:someValuesFrom biolink:PhenotypicQuality . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:LifeStage ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:LifeStage . [] a owl:Restriction ; - rdfs:subClassOf biolink:PairwiseMolecularInteraction ; + rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PairwiseMolecularInteraction . + owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Case ; + rdfs:subClassOf biolink:ChemicalAffectsGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Case . + owl:someValuesFrom biolink:ChemicalAffectsGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicFeature ; + rdfs:subClassOf biolink:FoodAdditive ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicFeature . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ActivityAndBehavior . + owl:someValuesFrom biolink:FoodAdditive . [] a owl:Restriction ; - rdfs:subClassOf biolink:CorrelatedGeneToDiseaseAssociation ; + rdfs:subClassOf biolink:PhenotypicFeatureToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CorrelatedGeneToDiseaseAssociation . + owl:someValuesFrom biolink:PhenotypicFeatureToPhenotypicFeatureAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_biological_sequence ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_biological_sequence ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Outcome ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_biological_sequence ] ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity . + owl:someValuesFrom biolink:EntityToOutcomeAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismalEntityAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:GenomicBackgroundExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismalEntityAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:GenomicBackgroundExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellularOrganism ; + rdfs:subClassOf biolink:ChiSquaredAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellularOrganism . + owl:someValuesFrom biolink:ChiSquaredAnalysisResult . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PathologicalEntityMixin . + rdfs:subClassOf biolink:EntityToPhenotypicFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToEnvironmentAssociation ; + rdfs:subClassOf biolink:Disease ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToEnvironmentAssociation . + owl:someValuesFrom biolink:Disease . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:ChemicalGeneInteractionAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:ChemicalGeneInteractionAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalMeasurement ; + rdfs:subClassOf biolink:NamedThing ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalMeasurement . + owl:someValuesFrom biolink:NamedThing . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:CausalGeneToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:CausalGeneToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Human ; + rdfs:subClassOf biolink:InformationContentEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Human . + owl:someValuesFrom biolink:InformationContentEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChiSquaredAnalysisResult ; + rdfs:subClassOf biolink:ClinicalAttribute ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChiSquaredAnalysisResult . + owl:someValuesFrom biolink:ClinicalAttribute . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation ; + rdfs:subClassOf biolink:SequenceVariant ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . + owl:someValuesFrom biolink:SequenceVariant . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonInteraction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:SensitivityQuantifier . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:BiologicalSex ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonInteraction . + owl:someValuesFrom biolink:BiologicalSex . [] a owl:Restriction ; - rdfs:subClassOf biolink:ReactionToCatalystAssociation ; + rdfs:subClassOf biolink:BiologicalProcess ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ReactionToCatalystAssociation . + owl:someValuesFrom biolink:BiologicalProcess . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneToPhenotypicFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneToPhenotypicFeatureAssociation . [] a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct . + owl:someValuesFrom biolink:SpecificityQuantifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalCourse ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneOrGeneProduct . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalCourse . + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Drug ; + rdfs:subClassOf biolink:Fungus ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Drug . + owl:someValuesFrom biolink:Fungus . [] a owl:Restriction ; - rdfs:subClassOf biolink:AdministrativeEntity ; + rdfs:subClassOf biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AdministrativeEntity . + owl:someValuesFrom biolink:GeneToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:CausalGeneToDiseaseAssociation ; + rdfs:subClassOf biolink:VariantToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CausalGeneToDiseaseAssociation . + owl:someValuesFrom biolink:VariantToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:CodingSequence ; + rdfs:subClassOf biolink:Cell ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CodingSequence . + owl:someValuesFrom biolink:Cell . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ExposureEvent ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToExposureEventAssociationMixin . + rdfs:subClassOf biolink:CorrelatedGeneToDiseaseAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:CorrelatedGeneToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalToChemicalDerivationAssociation ; + rdfs:subClassOf biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalToChemicalDerivationAssociation . + owl:someValuesFrom biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:PreprintPublication ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PreprintPublication . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ConfidenceLevel ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ConfidenceLevel . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:RelativeFrequencyAnalysisResult ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:RelativeFrequencyAnalysisResult . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:SequenceVariant ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ] ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin . + owl:someValuesFrom biolink:VariantToEntityAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:DrugExposure ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:DrugExposure . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ComplexChemicalExposure ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ComplexChemicalExposure . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:synonym ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PhenotypicFeature ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:xref ], [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:sex_qualifier ] ; + owl:onProperty biolink:synonym ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin . + owl:someValuesFrom biolink:GeneProductMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Gene ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Gene . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:phenotypic_state ], + [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:phenotypic_state ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:expression_site ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:expression_site ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:expression_site ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ] ; + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:quantifier_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:quantifier_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:phenotypic_state ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin . + owl:someValuesFrom biolink:GeneExpressionMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:MolecularActivityToMolecularActivityAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:MolecularActivityToMolecularActivityAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Bacterium ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Bacterium . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:MaterialSampleDerivationAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:MaterialSampleDerivationAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ExposureEventToOutcomeAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ExposureEventToOutcomeAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:DiagnosticAid ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:DiagnosticAid . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:RetrievalSource ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:RetrievalSource . + +[] a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PathologicalEntityMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:MolecularMixture ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:MolecularMixture . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:CellLineAsAModelOfDiseaseAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:CellLineAsAModelOfDiseaseAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:AnatomicalEntity ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:AnatomicalEntity . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:SequenceAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:SequenceAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:BehavioralExposure ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:BehavioralExposure . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:StudyResult ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:StudyResult . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Genome ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Genome . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ] ; + owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToFeatureOrDiseaseQualifiersMixin . + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:MaterialSample ; + rdfs:subClassOf biolink:DiseaseToExposureEventAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MaterialSample . + owl:someValuesFrom biolink:DiseaseToExposureEventAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Patent ; + rdfs:subClassOf biolink:Polypeptide ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Patent . + owl:someValuesFrom biolink:Polypeptide . [] a owl:Restriction ; - rdfs:subClassOf biolink:DrugLabel ; + rdfs:subClassOf biolink:ExposureEventToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugLabel . + owl:someValuesFrom biolink:ExposureEventToPhenotypicFeatureAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToLocationAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ChemicalToChemicalAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ChemicalToChemicalAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:PlanetaryEntity ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PlanetaryEntity . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:SeverityValue ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:SeverityValue . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:Case ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ] ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityToEntityAssociationMixin . + owl:someValuesFrom biolink:CaseToEntityAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:SocioeconomicExposure ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:SocioeconomicExposure . [] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:timepoint ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:timepoint ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:time ; + owl:onProperty biolink:timepoint ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:RelationshipQuantifier . + owl:someValuesFrom biolink:ExposureEvent . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeographicLocation ; + rdfs:subClassOf biolink:GeneticInheritance ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeographicLocation . + owl:someValuesFrom biolink:GeneticInheritance . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:Outcome . + rdfs:subClassOf biolink:GeneAffectsChemicalAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneAffectsChemicalAssociation . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneProductIsoformMixin . + rdfs:subClassOf biolink:Serial ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Serial . [] a owl:Restriction ; - rdfs:subClassOf biolink:DrugToGeneAssociation ; + rdfs:subClassOf biolink:EnvironmentalProcess ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugToGeneAssociation . + owl:someValuesFrom biolink:EnvironmentalProcess . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:MolecularEntity ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:MolecularEntity . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:PairwiseMolecularInteraction ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PairwiseMolecularInteraction . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:BehavioralFeature ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:BehavioralFeature . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:PathologicalAnatomicalExposure ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PathologicalAnatomicalExposure . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Activity ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Activity . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:SiRNA ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:SiRNA . [] a owl:Restriction ; rdfs:subClassOf biolink:Behavior ; @@ -14498,37 +14442,93 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:Behavior . [] a owl:Restriction ; - rdfs:subClassOf biolink:BioticExposure ; + rdfs:subClassOf biolink:ChemicalToChemicalDerivationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BioticExposure . + owl:someValuesFrom biolink:ChemicalToChemicalDerivationAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToGeneExpressionAssociation ; + rdfs:subClassOf biolink:GeneToGoTermAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToGeneExpressionAssociation . + owl:someValuesFrom biolink:GeneToGoTermAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GrossAnatomicalStructure ; + rdfs:subClassOf biolink:GeneToGeneProductRelationship ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GrossAnatomicalStructure . + owl:someValuesFrom biolink:GeneToGeneProductRelationship . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:DrugLabel ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:DrugLabel . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Device ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Device . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ClinicalMeasurement ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ClinicalMeasurement . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureExposure ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureExposure . [] a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SpecificityQuantifier . + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct . [] a owl:Restriction ; - rdfs:subClassOf biolink:DruggableGeneToDiseaseAssociation ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Genotype ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Article ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DruggableGeneToDiseaseAssociation . + owl:someValuesFrom biolink:Article . [] a owl:Restriction ; - rdfs:subClassOf biolink:ProteinFamily ; + rdfs:subClassOf biolink:MacromolecularMachineToBiologicalProcessAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProteinFamily . + owl:someValuesFrom biolink:MacromolecularMachineToBiologicalProcessAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeographicExposure ; + rdfs:subClassOf biolink:ClinicalTrial ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeographicExposure . + owl:someValuesFrom biolink:ClinicalTrial . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonAssociation . diff --git a/project/prefixmap/biolink_model_prefix_map.json b/project/prefixmap/biolink_model_prefix_map.json index 5319bdeff..ffc9dfb5e 100644 --- a/project/prefixmap/biolink_model_prefix_map.json +++ b/project/prefixmap/biolink_model_prefix_map.json @@ -259,4 +259,4 @@ "skos": "http://www.w3.org/2004/02/skos/core#", "wgs": "http://www.w3.org/2003/01/geo/wgs84_pos", "xsd": "http://www.w3.org/2001/XMLSchema#" -} \ No newline at end of file +} diff --git a/project/protobuf/biolink_model.proto b/project/protobuf/biolink_model.proto index f564839c8..16f1a7df6 100644 --- a/project/protobuf/biolink_model.proto +++ b/project/protobuf/biolink_model.proto @@ -1,7 +1,3 @@ - syntax="proto3"; - package -// metamodel_version: 1.7.0 -// version: 4.2.2 // 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 message AccessibleDnaRegion { diff --git a/project/shacl/biolink_model.shacl.ttl b/project/shacl/biolink_model.shacl.ttl index c0a47a2cc..8339866d1 100644 --- a/project/shacl/biolink_model.shacl.ttl +++ b/project/shacl/biolink_model.shacl.ttl @@ -7,42 +7,31 @@ @prefix xsd: . biolink:AccessibleDnaRegion a sh:NodeShape ; - rdfs:subClassOf biolink:RegulatoryRegion ; 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:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - 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 long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:order 6 ; + 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:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:description "Alternate human-readable names for a thing" ; sh:order 7 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - 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 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:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:has_biological_sequence ], [ sh:class biolink:OrganismTaxon ; @@ -50,377 +39,460 @@ biolink:AccessibleDnaRegion a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], + 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 3 ; + sh:path biolink:in_taxon_label ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 9 ; - sh:path biolink:category ], + sh:order 1 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; 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:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 10 ; + sh:path rdf:type ] ; + sh:targetClass biolink:AccessibleDnaRegion . + +biolink:Activity a sh:NodeShape ; + sh:closed true ; + sh:description "An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; 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:datatype xsd:string ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 13 ; + sh:order 10 ; sh:path biolink:has_attribute ] ; - sh:targetClass biolink:AccessibleDnaRegion . + sh:targetClass biolink:Activity . biolink:ActivityAndBehavior a sh:NodeShape ; - rdfs:subClassOf biolink:Occurrent ; sh:closed false ; sh:description "Activity or behavior of any independent integral living, organization or mechanical actor in the world" ; sh:ignoredProperties ( rdf:type ) ; sh:targetClass biolink:ActivityAndBehavior . -biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityAssociation ; - 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." ; +biolink:AdministrativeEntity a sh:NodeShape ; + sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 6 ; + sh:path biolink:category ], + [ sh:description "a long-form human readable name for a thing" ; + 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 10 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier 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 "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ] ; + sh:targetClass biolink:AdministrativeEntity . + +biolink:AnatomicalEntityToAnatomicalEntityAssociation a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold 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:datatype xsd:boolean ; + 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 5 ; sh:path biolink:qualifiers ], [ sh:class biolink:AnatomicalEntity ; - sh:description "the structure at an earlier time" ; + 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: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:datatype xsd:string ; - 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:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource 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 IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:description "A 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:nodeKind sh:Literal ; sh:order 34 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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:datatype xsd:string ; + sh:description "Used to hold the 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:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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 6 ; - sh:path biolink:publications ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the 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:subject_category_closure ], + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold 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:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_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 18 ; - sh:path biolink:object_category ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 15 ; - 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 19 ; + 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 27 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + 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 36 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - 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:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "used to 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:knowledge_level ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 35 ; + 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:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:has_evidence ] ; + 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:datatype xsd:string ; + sh:description "Used to hold the 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:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category 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 17 ; - sh:path biolink:subject_category ], + sh:order 22 ; + 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 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold 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:AnatomicalEntity ; - sh:description "the structure at a later time" ; + sh:description "the structure at an earlier time" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + 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 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object 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:datatype xsd:string ; sh:description "used to 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:Literal ; sh:order 14 ; sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:id ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; 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 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ] ; - sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . - -biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityAssociation ; - 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 biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ 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 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 31 ; + 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 32 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; sh:order 19 ; 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 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + 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:OntologyClass ; - sh:description "Used to hold the 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 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:AnatomicalEntity ; - sh:description "the whole" ; + sh:description "the structure at a later time" ; 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:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -428,2442 +500,2349 @@ biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "used to 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:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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 36 ; - sh:path biolink:has_attribute ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - 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 25 ; + 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 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ 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:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ 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:AnatomicalEntity ; - sh:description "the part" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ 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:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], [ 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:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 17 ; + 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:nodeKind sh:Literal ; sh:order 34 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:boolean ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ] ; + 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:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the 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:AnatomicalEntity ; + sh:description "the part" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink: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:class biolink:RetrievalSource ; - sh:description "A list of 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:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - 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:order 14 ; + sh:path biolink:original_subject ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold 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:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], + sh:order 24 ; + 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 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 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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 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 "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ] ; - sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . - -biolink:Bacterium a sh:NodeShape ; - rdfs:subClassOf biolink:OrganismalEntity ; - 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:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path dct:description ], + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:description "Used to hold 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 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + 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:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 28 ; + sh:path biolink:p_value ], + [ 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:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 6 ; + sh:order 30 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 36 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "An intermediate aggregator resource 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 point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:Bacterium . - -biolink:BehaviorToBehavioralFeatureAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - 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:class biolink:BehavioralFeature ; - sh:description "behavioral feature that is the object of the association" ; + sh:path biolink:timepoint ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:anyURI ; - 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 34 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "used to 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:Literal ; sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "the whole" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_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 19 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 15 ; - 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 8 ; - sh:path biolink:has_evidence ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_direction_qualifier ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; + sh:description "Used to hold the object 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: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 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; + 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 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ] ; + sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . + +biolink:Annotation a sh:NodeShape ; + sh:closed false ; + sh:description "Biolink Model root class for entity annotations." ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:Annotation . + +biolink:Article a sh:NodeShape ; + sh:closed true ; + sh:description "a piece of writing on a particular topic presented as a stand-alone section of a larger publication" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:order 21 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + 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 "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 19 ; + sh:path biolink:iri ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 8 ; + sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + 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:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:order 1 ; + sh:path biolink:iso_abbreviation ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + 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:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 2 ; + sh:path biolink:volume ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:authors ], + [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:order 10 ; + sh:path dct:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 37 ; + sh:order 24 ; 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 20 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + sh:description "keywords tagging a publication" ; + sh:order 7 ; + sh:path biolink:keywords ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:string ; - sh:description "used to 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:license ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 23 ; + 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:nodeKind sh:Literal ; - sh:order 35 ; + sh:order 22 ; sh:path rdfs:label ], - [ sh:datatype ; - 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:Literal ; - sh:order 48 ; - 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:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:summary ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:path biolink:creation_date ], + [ sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 0 ; + sh:path biolink:published_in ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], + sh:order 13 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; + 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:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 25 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 12 ; + 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 9 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 15 ; + sh:path biolink:provided_by ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], + sh:order 16 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + 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:nodeKind sh:Literal ; - sh:order 31 ; + sh:order 18 ; sh:path biolink:id ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 17 ; + sh:path biolink:synonym ] ; + 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:datatype xsd:string ; + 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:datatype xsd:string ; sh:description "Used to hold 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:Literal ; - sh:order 25 ; + sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_quotient ], + [ 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:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 24 ; - 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 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to 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:Literal ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], + sh:order 14 ; + 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 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; + sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + 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 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 35 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + 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 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - 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:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:qualified_predicate ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold 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:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 29 ; - sh:path biolink:p_value ], - [ sh:class biolink:Behavior ; - sh:description "behavior that is the subject of the association" ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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:datatype xsd:string ; + sh:description "An intermediate aggregator resource 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:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_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 point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ 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:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - 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 6 ; + sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + [ sh:datatype xsd:string ; + sh:description "used to 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:Literal ; - sh:order 39 ; - 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 7 ; - sh:path biolink:publications ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:has_total ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the 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:targetClass biolink:BehaviorToBehavioralFeatureAssociation . - -biolink:BehavioralExposure a sh:NodeShape ; - rdfs:subClassOf biolink:Attribute ; - sh:closed true ; - sh:description "A behavioral exposure is a factor relating to behavior impacting an individual." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:minCount 1 ; sh:order 1 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:description "Used to hold the biolink class/category 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 biolink:has_attribute_type ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - 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:object_category ] ; + 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:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ], + sh:path dct:description ], [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; - sh:order 14 ; + sh:order 12 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; + sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; + sh:order 4 ; sh:path biolink:full_name ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 biolink:in_taxon_label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ] ; - sh:targetClass biolink:BehavioralExposure . - -biolink:BehavioralOutcome a sh:NodeShape ; - sh:closed true ; - sh:description "An outcome resulting from an exposure event which is the manifestation of human behavior." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:BehavioralOutcome . - -biolink:BioticExposure a sh:NodeShape ; - rdfs:subClassOf biolink:Attribute ; - 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:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 0 ; + sh:path biolink:in_taxon ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; + sh:order 8 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:full_name ], + 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:datatype xsd:string ; sh:description "A unique 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:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ] ; + 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:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 39 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 9 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an 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:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:order 15 ; + 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 33 ; + sh:path biolink:category ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:BioticExposure . - -biolink:Book a sh:NodeShape ; - rdfs:subClassOf biolink:Publication ; - 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:datatype xsd:string ; - sh:description "executive summary of a publication" ; + sh:order 44 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object 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:datatype xsd:string ; + sh:description "Used to hold the subject 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:datatype xsd:double ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:summary ], - [ 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:order 41 ; + 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 0 ; - sh:path biolink:authors ], + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 19 ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 36 ; sh:path dct:description ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:has_total ], [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:keywords ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "Used to hold 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:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:minCount 1 ; sh:order 12 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Behavior ; + sh:description "behavior that is the subject of the association" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path dct:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "A unique 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:Literal ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 31 ; + 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:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:mesh_terms ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; + sh:minCount 1 ; sh:order 1 ; - sh:path biolink:pages ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 18 ; - sh:path rdfs:label ], + sh:path rdf:predicate ], [ sh:datatype xsd:string ; + sh:description "Used to hold the 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:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:format ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; + sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; sh:order 10 ; - sh:path biolink:creation_date ], + 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:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is 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:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:rights ], + sh:order 45 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "Should generally be set to an ontology class defined term for 'book'." ; - sh:nodeKind sh:Literal ; - sh:order 17 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; + sh:order 48 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 32 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Books should have industry-standard identifier such as from ISBN." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:id ] ; - sh:targetClass biolink:Book . - -biolink:BookChapter a sh:NodeShape ; - rdfs:subClassOf biolink:Publication ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - 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 13 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + 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:Literal ; - sh:order 21 ; - sh:path rdfs:label ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - 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 "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:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:pages ], + sh:order 47 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:rights ], - [ sh:datatype xsd:anyURI ; - sh:description "The enclosing parent book containing the chapter should have industry-standard identifier from ISBN." ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:class biolink:BehavioralFeature ; + sh:description "behavioral feature that is the object of the association" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:published_in ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; + sh:order 46 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - 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:order 29 ; + sh:path biolink:p_value ], + [ 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:Literal ; - sh:order 1 ; - sh:path biolink:volume ], + sh:order 16 ; + 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 7 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:format ], + sh:description "An intermediate aggregator resource 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:datatype xsd:string ; - sh:description "a human-readable description of an 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:nodeKind sh:Literal ; - sh:order 22 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:full_name ], + sh:order 4 ; + sh:path biolink:negated ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; + sh:order 38 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:nodeKind sh:Literal ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the 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:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; sh:order 6 ; - sh:path biolink:keywords ], + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + sh:description "Used to hold the 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:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 43 ; + sh:path biolink:subject_aspect_qualifier ] ; + 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:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:summary ], + sh:path biolink:iri ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:synonym ], + [ 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 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 13 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; sh:order 14 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:mesh_terms ], - [ sh:datatype xsd:string ; - sh:description "chapter of a book" ; + sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:chapter ], - [ 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: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:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; sh:order 3 ; - sh:path biolink:authors ], + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:category ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:order 12 ; + 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:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:type ] ; - sh:targetClass biolink:BookChapter . + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:BehavioralExposure . -biolink:CaseToEntityAssociationMixin a sh:NodeShape ; +biolink:BehavioralOutcome a sh:NodeShape ; + sh:closed true ; + sh:description "An outcome resulting from an exposure event which is the manifestation of human behavior." ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:BehavioralOutcome . + +biolink:BiologicalEntity a sh:NodeShape ; sh:closed false ; - sh:description "An abstract association for use where the case is the subject" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Case ; - sh:description "the case (e.g. patient) that has the property" ; + sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier 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:maxCount 1 ; + sh:order 11 ; + 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 biolink:in_taxon_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 rdf:subject ], - [ 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: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 8 ; + sh:path biolink:category ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + 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:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ] ; - sh:targetClass biolink:CaseToEntityAssociationMixin . + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:targetClass biolink:BiologicalEntity . -biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; +biolink:BiologicalProcessOrActivity 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: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:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ 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 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:anyURI ; - 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 13 ; + sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ], + sh:order 14 ; + sh:path dct:description ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_input ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:order 12 ; + 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 11 ; + sh:path biolink:category ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_output ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:has_total ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; + sh:order 5 ; + sh:path biolink:in_taxon_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 2 ; + sh:path biolink:enabled_by ] ; + sh:targetClass biolink:BiologicalProcessOrActivity . + +biolink:BioticExposure a sh:NodeShape ; + sh:closed true ; + sh:description "An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses)." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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: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:datatype xsd:double ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_quotient ], + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier 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 "Used to hold the 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 attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], + 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:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; + sh:order 12 ; sh:path rdf:type ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - 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:order 13 ; + 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:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:nodeKind sh:IRI ; sh:order 4 ; - sh:path biolink:negated ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - 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:path biolink:has_qualitative_value ], + [ 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 9 ; + sh:path biolink:full_name ] ; + 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:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], + sh:path dct:type ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:knowledge_source ], + sh:path biolink:format ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + sh:description "keywords tagging a publication" ; + sh:order 3 ; + sh:path biolink:keywords ], [ sh:datatype xsd:string ; - sh:description "used to 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 "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:datatype xsd:string ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 2 ; + sh:path biolink:summary ], + [ sh:datatype xsd:string ; + sh:description "Books should have industry-standard identifier such as from ISBN." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 14 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_closure ], + sh:description "Should generally be set to an ontology class defined term for 'book'." ; + sh:order 17 ; + sh:path rdf:type ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 4 ; + sh:path biolink:mesh_terms ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 37 ; + sh:order 20 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; + sh:order 10 ; + 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:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:order 19 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 21 ; + sh:path biolink:deprecated ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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 12 ; + 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:nodeKind sh:Literal ; - sh:order 10 ; - 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 15 ; + sh:path biolink:iri ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 18 ; - sh:path biolink:subject_category ], + sh:path rdfs:label ], [ sh:datatype xsd:string ; - 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: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:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 16 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Case ; - sh:description "the case (e.g. patient) that has the property" ; + sh:order 8 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:targetClass biolink:Book . + +biolink:BookChapter 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 23 ; + sh:path biolink:has_attribute ], + [ sh:description "The enclosing parent book containing the chapter should have industry-standard identifier from ISBN." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path rdf:subject ], + sh:path biolink:published_in ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:datatype ; - 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:Literal ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 11 ; + sh:path biolink:rights ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], + sh:order 22 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + 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:nodeKind sh:Literal ; - sh:order 31 ; + sh:order 17 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 12 ; + sh:path biolink:format ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:deprecated ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 7 ; + sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ], + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "used to 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 "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:order 9 ; + sh:path dct:type ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + 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:datatype xsd:string ; + sh:description "keywords tagging a publication" ; + sh:order 6 ; + sh:path biolink:keywords ], + [ sh:datatype xsd:string ; + sh:description "chapter of a book" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - 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 7 ; - sh:path biolink:publications ], + sh:order 2 ; + sh:path biolink:chapter ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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 20 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + 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:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:order 1 ; + sh:path biolink:volume ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:datatype xsd:date ; + 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:datatype xsd:string ; - 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:description "The value in this node property represents the knowledge provider that created or assembled the node 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: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 "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:qualified_predicate ] ; - sh:targetClass biolink:CaseToPhenotypicFeatureAssociation . + sh:order 18 ; + sh:path biolink:iri ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:order 21 ; + 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 19 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:summary ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 16 ; + sh:path biolink:synonym ] ; + sh:targetClass biolink:BookChapter . -biolink:CausalGeneToDiseaseAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:GeneToDiseaseAssociation ; - sh:closed true ; +biolink:CaseToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:description "An abstract association for use where the case is the subject" ; 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: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 9 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Case ; + sh:description "the case (e.g. patient) that has the property" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:id ], + 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:targetClass biolink:CaseToEntityAssociationMixin . + +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:datatype xsd:double ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object 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 "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ], + sh:order 44 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:string ; + sh:description "Used to hold 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:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 36 ; + 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:description "Used to hold the 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:object_category_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:category ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is shown to cause the disease." ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Case ; + sh:description "the case (e.g. patient) that has the property" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; + sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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 20 ; + sh:path biolink:subject_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:Literal ; - sh:order 11 ; - 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 24 ; - sh:path biolink:subject_category_closure ], + sh:order 3 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 38 ; - sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:object_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:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 12 ; + sh:order 10 ; 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 8 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 26 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 10 ; + sh:order 8 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - 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: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 5 ; - sh:path biolink:sex_qualifier ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:order 48 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 29 ; + sh:path biolink:p_value ], [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_count ], + sh:order 40 ; + sh:path biolink:has_total ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:time ; - 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:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:timepoint ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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 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 high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_namespace ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], + sh:order 45 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - 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 namespace 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:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:anyURI ; - 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 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 33 ; + 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:nodeKind sh:Literal ; - sh:order 18 ; + sh:order 16 ; 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 30 ; - sh:path biolink:retrieval_source_ids ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; 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:nodeKind sh:Literal ; sh:order 47 ; sh:path biolink:qualified_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 20 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_total ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; + sh:order 4 ; 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 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - 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 11 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to 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:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_object ], + sh:order 9 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh: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:object_category ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "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 3 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 6 ; + 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 28 ; + 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:datatype xsd:double ; sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; + sh:order 42 ; sh:path biolink:has_percentage ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ] ; - sh:targetClass biolink:CausalGeneToDiseaseAssociation . - -biolink:Cell a sh:NodeShape ; - rdfs:subClassOf biolink:AnatomicalEntity ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:minCount 1 ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 37 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:minCount 1 ; sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - 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:agent_type ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the 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:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 43 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 46 ; + sh:path biolink:object_direction_qualifier ], + [ 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:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ] ; - sh:targetClass biolink:Cell . + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ] ; + sh:targetClass biolink:CaseToPhenotypicFeatureAssociation . -biolink:CellLineAsAModelOfDiseaseAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation ; +biolink:CausalGeneToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:property [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; + sh:order 48 ; sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + 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:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], + sh:order 47 ; + sh:path biolink:qualified_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 18 ; + 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 9 ; + sh:path biolink:publications ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:p_value ], [ 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:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 44 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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 39 ; + sh:path biolink:has_attribute ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:anyURI ; - 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 37 ; + sh:path rdfs:label ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:minCount 1 ; sh:order 15 ; - sh:path biolink:original_predicate ], + sh:path biolink:agent_type ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:has_count ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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 "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 36 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 7 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 43 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - 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 19 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - 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:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:qualified_predicate ], - [ 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:order 11 ; + sh:path biolink:knowledge_source ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; + sh:order 14 ; sh:path biolink:knowledge_level ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:has_total ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "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 3 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - 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 23 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 33 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is 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:order 20 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - 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:description "Used to hold 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:retrieval_source_ids ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + 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:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 5 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:object_direction_qualifier ], + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to 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:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + 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 21 ; + sh:order 24 ; sh:path biolink:subject_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is shown to cause the disease." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - 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 22 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; + sh:description "An intermediate aggregator resource 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:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label 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:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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:subject_label_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ 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:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is 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:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:order 21 ; + sh:path biolink:object_category ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 38 ; - sh:path biolink:subject_aspect_qualifier ], + 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 35 ; + 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 30 ; + 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: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:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 40 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - 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 6 ; - sh:path biolink:publications ], + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:id ], + sh:order 17 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "used to 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:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 26 ; + 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 39 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 34 ; + sh:path biolink: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 25 ; + sh:path biolink:object_category_closure ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:timepoint ] ; + sh:targetClass biolink:CausalGeneToDiseaseAssociation . + +biolink:Cell 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 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:path biolink:category ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ 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:order 7 ; + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The relationship to 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:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; + sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ] ; - sh:targetClass biolink:CellLineAsAModelOfDiseaseAssociation . - -biolink:CellLineToEntityAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:description "An relationship between a cell line and another entity" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:CellLine ; - 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 long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:order 9 ; + 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 rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:path biolink:in_taxon ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ] ; - sh:targetClass biolink:CellLineToEntityAssociationMixin . + sh:order 12 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:Cell . -biolink:ChemicalAffectsGeneAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; +biolink:CellLineAsAModelOfDiseaseAssociation 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:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; - sh:in ( "metabolite" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_derivative_qualifier ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:property [ 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:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 28 ; - sh:path biolink:timepoint ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:path biolink:p_value ], + [ 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:object_part_qualifier ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; - 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 biolink:frequency_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 47 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "used to 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 32 ; sh:path biolink:category ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:subject_direction_qualifier ], + sh:order 41 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; 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:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 42 ; sh:path biolink:qualified_predicate ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 16 ; - 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:order 30 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; - sh:path biolink: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 20 ; - sh:path biolink:qualifiers ], - [ 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 12 ; - sh:path biolink:anatomical_context_qualifier ], - [ sh:class biolink:AnatomicalEntity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:object_context_qualifier ], - [ sh:class biolink:AnatomicalEntity ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:subject_context_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 52 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "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 8 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 30 ; - sh:path biolink:original_predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; sh:order 27 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path rdf:type ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:path biolink:retrieval_source_ids ], + [ 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 15 ; + sh:order 0 ; sh:path rdf:subject ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_part_qualifier ], + sh:order 38 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 23 ; - sh:path biolink:knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:path biolink:subject_namespace ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 26 ; - sh:path biolink:knowledge_level ], + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 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 32 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:iri ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "used to 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:Literal ; - sh:order 31 ; + sh:order 16 ; sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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 34 ; + 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 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 35 ; + sh:order 20 ; sh:path biolink:object_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; - 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 42 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh: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:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:species_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "used to 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 35 ; + sh:path dct:description ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - 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:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 36 ; - 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 33 ; - sh:path biolink:object_category ], + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:nodeKind sh:Literal ; sh:order 24 ; - sh:path biolink:primary_knowledge_source ], + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; + sh:order 4 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:id ], - [ 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: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:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; + sh:nodeKind sh:IRI ; sh:order 17 ; - sh:path rdf:object ], + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path dct:description ], + sh:order 39 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:negated ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "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 boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_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 37 ; - sh:path biolink:object_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:maxCount 1 ; - sh:order 11 ; - sh:path biolink:causal_mechanism_qualifier ], + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 38 ; - 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:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; + sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + [ 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:object_form_or_variant_qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 31 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:CellLineAsAModelOfDiseaseAssociation . + +biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:adjusted_p_value ], + sh:order 31 ; + 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:datatype xsd:string ; - sh:description "Used to hold 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:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 51 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:ChemicalAffectsGeneAssociation . - -biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - 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 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the 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:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - 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 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an 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:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], - [ 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 8 ; + 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:Publication ; + sh:description "One or more 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 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object 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:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the 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:datatype xsd:string ; + 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 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 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to 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 subject 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:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "used to 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:Literal ; 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 6 ; - sh:path biolink:publications ], - [ 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:datatype xsd:string ; + sh:description "A unique identifier 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 human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Used to hold 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:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - 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 10 ; + 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:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -2871,16 +2850,6 @@ biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the 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:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -2888,821 +2857,623 @@ biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the 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:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 28 ; - sh:path biolink:p_value ] ; - sh:targetClass biolink:ChemicalEntityAssessesNamedThingAssociation . - -biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - sh:closed true ; - sh:description "A regulatory relationship between two genes" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:path biolink:p_value ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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 19 ; + sh:order 18 ; sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ 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 biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:path rdf:subject ] ; + sh:targetClass biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . + +biolink:CellLineToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:description "An relationship between a cell line and another entity" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:CellLine ; + 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:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - 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:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ 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: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:nodeKind sh:BlankNodeOrIRI ; sh:order 1 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 2 ; + sh:path rdf:object ] ; + sh:targetClass biolink:CellLineToEntityAssociationMixin . + +biolink:CellularOrganism a sh:NodeShape ; + sh:closed true ; + sh:description "" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:nodeKind sh:Literal ; - sh:order 32 ; + sh:order 7 ; 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 22 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; + sh:order 11 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "the direction is always from regulator to regulated" ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_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:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; + 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 3 ; - sh:path rdf:object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], - [ 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:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "used to 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:nodeKind sh:Literal ; - sh:order 17 ; - 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 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: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:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 16 ; - 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: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 18 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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:has_attribute ] ; + sh:targetClass biolink:CellularOrganism . + +biolink:ChemicalAffectsGeneAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh: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:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], + sh:minCount 1 ; + sh:order 16 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; sh:order 31 ; - sh:path biolink:id ], + sh:path biolink:original_object ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; + sh:order 27 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ] ; - sh:targetClass biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . - -biolink:ChemicalEntityOrProteinOrPolypeptide a sh:NodeShape ; - sh:closed false ; - sh:description "A union of chemical entities and children, and protein and polypeptide. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:ChemicalEntityOrProteinOrPolypeptide . - -biolink:ChemicalGeneInteractionAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - 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:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 18 ; + sh:order 25 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:IRI ; + sh:order 32 ; + 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 37 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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 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:Literal ; - sh:order 17 ; - sh:path biolink:primary_knowledge_source ], + sh:order 29 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 26 ; + sh:order 33 ; sh:path biolink:object_category ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + 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:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - 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 13 ; - sh:path biolink:qualifiers ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 48 ; + sh:path rdf:type ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 44 ; + sh:path biolink:adjusted_p_value ], [ 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 7 ; + sh:order 12 ; sh:path biolink:anatomical_context_qualifier ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - 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 36 ; + 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 14 ; + sh:order 21 ; 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:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 33 ; + sh:order 40 ; sh:path biolink:subject_label_closure ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path rdf:type ], + sh:order 50 ; + sh:path dct:description ], + [ sh:class biolink:AnatomicalEntity ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:subject_context_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; sh:order 39 ; - sh:path biolink:iri ], + 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 15 ; + sh:order 22 ; sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category ], + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 41 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object 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:object_closure ], [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; sh:in ( "metabolite" ) ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:subject_derivative_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 35 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 24 ; - sh:path biolink:original_object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 44 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the 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 29 ; - sh:path biolink:subject_category_closure ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + [ 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 5 ; - sh:path biolink:object_part_qualifier ], + sh:order 11 ; + sh:path biolink:causal_mechanism_qualifier ], [ sh:datatype xsd:string ; - 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:Literal ; - sh:order 9 ; - sh:path rdf:predicate ], - [ sh:class biolink:AnatomicalEntity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:subject_context_qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:adjusted_p_value ], + sh:order 19 ; + sh:path biolink: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:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:object_category_closure ], + sh:order 20 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; + sh:order 43 ; sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 31 ; - sh:path biolink:subject_namespace ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_form_or_variant_qualifier ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical entity or entity that is an interactor" ; + sh:order 52 ; + sh:path biolink:deprecated ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "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 8 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:object_namespace ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:order 5 ; + sh:path biolink:subject_direction_qualifier ], + [ 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:subject_part_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 46 ; + 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:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 30 ; + sh:path biolink:original_predicate ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path dct:description ], + sh:order 28 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; + sh:order 23 ; sh:path biolink:knowledge_source ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 49 ; + 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 42 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:object_form_or_variant_qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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 24 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold 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:Literal ; sh:order 38 ; - sh:path biolink:id ], - [ sh:class biolink:AnatomicalEntity ; + 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 47 ; + sh:path biolink:category ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:object_context_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 14 ; + sh:path biolink:species_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 19 ; - sh:path biolink:knowledge_level ], + sh:order 45 ; + sh:path biolink:id ], [ 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:BlankNodeOrIRI ; - sh:order 10 ; + sh:order 17 ; sh:path rdf:object ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; + 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:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 51 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 34 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:path biolink:subject_closure ], + [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:qualifier ], + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:object_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + 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:nodeKind sh:Literal ; - sh:order 42 ; - sh:path rdfs:label ], + sh:order 13 ; + sh:path biolink:qualified_predicate ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; + 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:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 20 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 22 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 23 ; - sh:path biolink:original_predicate ] ; - sh:targetClass biolink:ChemicalGeneInteractionAssociation . - -biolink:ChemicalOrDrugOrTreatment a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:ChemicalOrDrugOrTreatment . + sh:order 26 ; + sh:path biolink:knowledge_level ] ; + sh:targetClass biolink:ChemicalAffectsGeneAssociation . -biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation ; +biolink:ChemicalEntityAssessesNamedThingAssociation 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, typically (but not always) undesirable effect." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:class biolink:RetrievalSource ; + sh:description "A list of 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 23 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; + sh:order 4 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 31 ; + 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 19 ; + sh:order 18 ; sh:path biolink:object_category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ 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:datatype xsd:string ; + sh:description "used to 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:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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: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:path biolink:knowledge_source ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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 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:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; + sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the 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:Publication ; - sh:description "One or more 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:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:description "" ; - sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:FDA_adverse_event_level ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:timepoint ], + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "used to 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:Literal ; - sh:order 15 ; + sh:order 14 ; sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 30 ; + sh:path biolink:id ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; + sh:order 28 ; sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ 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:Literal ; - sh:order 31 ; - sh:path biolink:id ], + 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 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 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - 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 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - 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 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:Publication ; + sh:description "One or more 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 ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; + sh:order 6 ; + 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:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; + sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], + [ 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:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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:nodeKind sh:Literal ; sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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 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:nodeKind sh:Literal ; - sh:order 25 ; - 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:order 34 ; + 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 28 ; - sh:path biolink:retrieval_source_ids ] ; - sh:targetClass biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . + sh:order 5 ; + 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 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource 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:ChemicalEntityAssessesNamedThingAssociation . -biolink:ChemicalToChemicalDerivationAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:ChemicalToChemicalAssociation ; +biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape ; sh:closed true ; - sh:description "A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: IF R has-input C1 AND R has-output C2 AND R enabled-by P AND R type Reaction THEN C1 derives-into C2 catalyst qualifier P" ; + sh:description "A regulatory relationship between two genes" ; 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 "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical." ; - sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; - sh:path biolink:catalyst_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - 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:Literal ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:path biolink:object_direction_qualifier ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -3711,10478 +3482,9741 @@ biolink:ChemicalToChemicalDerivationAssociation a sh:NodeShape ; sh:order 12 ; sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "used to 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 "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_object ], + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_closure ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "Used to hold 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:Literal ; sh:order 24 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - 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 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ 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:Literal ; - sh:order 4 ; - sh:path biolink:negated ], + sh:order 16 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 23 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], + sh:order 25 ; + 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 6 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 33 ; + sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ 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:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 1 ; + sh:path rdf: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 ; sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - 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:negated ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 35 ; + 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 22 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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:Publication ; sh:description "One or more 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:datatype xsd:string ; + sh:description "used to 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:datatype xsd:string ; + sh:description "Used to hold the object 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:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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: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:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the upstream chemical entity" ; + sh:minCount 1 ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:description "the direction is always from regulator to regulated" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - 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 10 ; + 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:description "Used to hold the biolink class/category of an association. This is 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_closure ], - [ sh:datatype xsd:anyURI ; - 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 ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the downstream chemical entity" ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category 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 3 ; - sh:path rdf:object ] ; - sh:targetClass biolink:ChemicalToChemicalDerivationAssociation . - -biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - 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:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + 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:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:agent_type ] ; + sh:targetClass biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . + +biolink:ChemicalEntityOrProteinOrPolypeptide a sh:NodeShape ; + sh:closed false ; + sh:description "A union of chemical entities and children, and protein and polypeptide. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities." ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:ChemicalEntityOrProteinOrPolypeptide . + +biolink:ChemicalEntityToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:description "An interaction between a chemical entity and another entity" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:boolean ; - 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: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:nodeKind sh:Literal ; - 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:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity that is an interactor" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ] ; + sh:targetClass biolink:ChemicalEntityToEntityAssociationMixin . + +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:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + 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:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; sh:order 6 ; - sh:path biolink:publications ], + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - 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:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 36 ; + sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path dct:description ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; 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 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "the disease or phenotype that is affected by the chemical" ; + 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: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. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:datatype xsd:string ; + sh:order 12 ; + 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 2 ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path biolink:has_quantitative_value ] ; + sh:targetClass biolink:ChemicalExposure . + +biolink:ChemicalGeneInteractionAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to 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 24 ; + sh:path biolink:original_object ], + [ 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:BlankNodeOrIRI ; + sh:order 10 ; 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 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink: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:nodeKind sh:Literal ; sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 45 ; + sh:path biolink:deprecated ], + [ 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:Literal ; - sh:order 1 ; + sh:order 9 ; sh:path rdf:predicate ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:timepoint ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; + sh:order 20 ; sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "used to 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 "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 41 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 12 ; + sh:path biolink:qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 30 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - 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 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; + sh:description "A unique 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:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 38 ; + sh:path biolink:id ], + [ 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:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - 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:class biolink:OntologyClass ; - sh:description "Used to hold the 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:anatomical_context_qualifier ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ] ; - sh:targetClass biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation . - -biolink:ChemicalToEntityAssociationMixin a sh:NodeShape ; - rdfs:subClassOf biolink:ChemicalEntityToEntityAssociationMixin ; - sh:closed false ; - sh:description "An interaction between a chemical entity and another entity" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ 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 43 ; + sh:path dct:description ], + [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; + sh:in ( "metabolite" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - 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:Literal ; - sh:order 1 ; - sh:path rdf:predicate ] ; - sh:targetClass biolink:ChemicalToEntityAssociationMixin . - -biolink:ChemicalToPathwayAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - sh:closed true ; - sh:description "An interaction between a chemical entity and a biological process or pathway." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of 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:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:path biolink:subject_derivative_qualifier ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; + sh:order 36 ; sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is 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:subject_category ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - 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 28 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 11 ; + sh:path biolink:negated ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; + 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:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - 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 6 ; - sh:path biolink:publications ], + sh:order 4 ; + sh:path biolink:object_form_or_variant_qualifier ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; + sh:order 19 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Pathway ; - sh:description "the pathway that is affected by the chemical" ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of 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 35 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 6 ; + sh:path biolink:object_context_qualifier ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; + 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:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 36 ; + sh:order 44 ; 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:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:subject_context_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 13 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "used to 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:nodeKind sh:Literal ; sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + 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 14 ; + sh:path biolink:publications ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - 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:order 5 ; + sh:path biolink:object_part_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 33 ; + 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:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 39 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 9 ; + sh:order 17 ; sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold 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:Literal ; - sh:order 23 ; + sh:order 31 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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 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 29 ; + 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:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; + sh:nodeKind sh:IRI ; sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical entity that is affecting the pathway" ; + sh:path biolink:object_category ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; + sh:order 8 ; sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the 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:datatype xsd:string ; + sh:description "Used to hold the subject 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_closure ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; + sh:order 18 ; 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 40 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ] ; - sh:targetClass biolink:ChemicalToPathwayAssociation . + sh:order 32 ; + 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 15 ; + sh:path biolink:has_evidence ] ; + sh:targetClass biolink:ChemicalGeneInteractionAssociation . -biolink:ChiSquaredAnalysisResult a sh:NodeShape ; - rdfs:subClassOf biolink:StudyResult ; +biolink:ChemicalMixture a sh:NodeShape ; sh:closed true ; - sh:description "A result of a chi squared analysis." ; + sh:description "A chemical mixture is a chemical entity composed of two or more molecular entities." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 8 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; + sh:property [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:full_name ], + 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 15 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; + sh:description "" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path biolink:license ], + sh:path biolink:is_supplement ], [ sh:datatype xsd:string ; + sh:order 16 ; + sh:path rdf:type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 10 ; + sh:path biolink:xref ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 12 ; + 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 8 ; + sh:path biolink:has_chemical_role ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + 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:nodeKind sh:Literal ; sh:order 2 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 18 ; sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; + sh:order 20 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:ChiSquaredAnalysisResult . - -biolink:ClinicalFinding a sh:NodeShape ; - rdfs:subClassOf biolink:PhenotypicFeature ; - 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:datatype xsd:string ; + 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:datatype xsd:boolean ; + sh:description "" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:is_toxic ], + [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; + sh:order 9 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - 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 3 ; + sh:path biolink:routes_of_delivery ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 6 ; + sh:order 13 ; sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - 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:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:order 19 ; + 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, 'clinical approval status.'" ; + 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:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; + sh:order 14 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:class biolink:ClinicalAttribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:ClinicalFinding . + sh:order 17 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:ChemicalMixture . -biolink:ClinicalMeasurement a sh:NodeShape ; - rdfs:subClassOf biolink:ClinicalAttribute ; +biolink:ChemicalOrDrugOrTreatment a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:ChemicalOrDrugOrTreatment . + +biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation 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: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:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; + sh:property [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; + sh:order 36 ; sh:path dct:description ], [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:description "Used to hold the biolink class/category 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 1 ; - sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + sh:order 19 ; + 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 6 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:id ], + sh:path biolink:qualifier ], + [ 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:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; + sh:order 38 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], + sh:order 14 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more 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 biolink:has_qualitative_value ], + sh:order 7 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ] ; - sh:targetClass biolink:ClinicalMeasurement . - -biolink:ClinicalModifier a sh:NodeShape ; - rdfs:subClassOf biolink:ClinicalAttribute ; - 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:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - 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 26 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - 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:Literal ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "An intermediate aggregator resource 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 33 ; + sh:path biolink:category ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an 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:OntologyClass ; + sh:description "Used to hold the 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:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:order 13 ; - sh:path biolink:has_attribute ], + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; + sh:minCount 1 ; + sh:order 31 ; + 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 8 ; - sh:path biolink:full_name ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + 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 3 ; - sh:path biolink:has_qualitative_value ], + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + 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:Literal ; - sh:order 4 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:ClinicalModifier . - -biolink:ClinicalTrial a sh:NodeShape ; - rdfs:subClassOf biolink:ClinicalEntity ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; + sh:order 35 ; sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "used to 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:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 6 ; - sh:path biolink:category ], + sh:order 15 ; + 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 28 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - 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 21 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:description "Used to hold 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:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; + sh:order 32 ; sh:path biolink:iri ], - [ 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 10 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:description "" ; + sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], + sh:order 3 ; + sh:path biolink:FDA_adverse_event_level ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ] ; - sh:targetClass biolink:ClinicalTrial . + sh:description "Used to hold 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:targetClass biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . -biolink:CodingSequence a sh:NodeShape ; - rdfs:subClassOf biolink:BiologicalEntity ; +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:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; + sh:order 24 ; + 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:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], + sh:order 32 ; + 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 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:minCount 1 ; sh:order 12 ; - sh:path dct:description ], + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the 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:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 7 ; + sh:order 31 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 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:Literal ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "used to 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:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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 17 ; + 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 33 ; + sh:path biolink:category ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:order 13 ; - sh:path biolink:has_attribute ], + sh:path biolink:agent_type ], + [ 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:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + 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 7 ; + sh:path biolink:publications ], + [ 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 biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ] ; - sh:targetClass biolink:CodingSequence . - -biolink:Cohort a sh:NodeShape ; - rdfs:subClassOf biolink:StudyPopulation ; - sh:closed true ; - sh:description "A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that samples a cohort, performing a cross-section at intervals through time." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - 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 rdf:object ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 1 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 4 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + 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 6 ; + sh:path biolink:qualifiers ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path dct:description ], + [ 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:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold 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:nodeKind sh:Literal ; + sh:order 16 ; + 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 22 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource 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 dct:description ], + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 38 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ 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:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:Cohort . + sh:order 5 ; + sh:path biolink: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 23 ; + sh:path biolink:object_category_closure ] ; + sh:targetClass biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . -biolink:CommonDataElement a sh:NodeShape ; - rdfs:subClassOf biolink:InformationContentEntity ; +biolink:ChemicalToChemicalAssociation 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: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:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - 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 10 ; + 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:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; sh:order 5 ; - sh:path biolink:xref ], + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "used to 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:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ 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:datatype xsd:string ; - 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 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:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:BlankNodeOrIRI ; + 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:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; + sh:description "Used to hold 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:Literal ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; + sh:description "Used to hold the 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:ChemicalEntity ; + sh:description "the chemical element that is the target of the statement" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ] ; - sh:targetClass biolink:CommonDataElement . - -biolink:ComplexChemicalExposure a sh:NodeShape ; - rdfs:subClassOf biolink:Attribute ; - 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:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path biolink:has_quantitative_value ], + 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 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:description "Used to hold the object 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:RetrievalSource ; + sh:description "A list of 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:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 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 21 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 13 ; + sh:order 36 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - 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:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - 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 20 ; + sh:path biolink:object_closure ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:order 35 ; + 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 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "A unique 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:Literal ; - sh:order 10 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], + sh:order 31 ; + sh:path biolink:iri ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ] ; - sh:targetClass biolink:ComplexChemicalExposure . + sh:description "Used to hold the subject 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:targetClass biolink:ChemicalToChemicalAssociation . -biolink:ComplexMolecularMixture a sh:NodeShape ; - rdfs:subClassOf biolink:ChemicalMixture ; +biolink:ChemicalToChemicalDerivationAssociation 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:description "A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: IF R has-input C1 AND R has-output C2 AND R enabled-by P AND R type Reaction THEN C1 derives-into C2 catalyst qualifier P" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:iri ], + sh:property [ 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:class biolink:Publication ; + sh:description "One or more 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:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:description "An intermediate aggregator resource 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:full_name ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 19 ; + sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - 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: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 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, 'clinical approval status.'" ; - 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: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 1 ; - sh:path biolink:highest_FDA_approval_status ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; sh:order 16 ; - sh:path rdf:type ], + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - 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 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:Literal ; - sh:order 13 ; - sh:path biolink:id ], + sh:order 25 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:is_supplement ], + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + 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:nodeKind sh:Literal ; - sh:order 18 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "" ; + sh:order 29 ; + sh:path biolink:p_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:order 33 ; + sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:order 36 ; + sh:path dct:description ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:order 14 ; + 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 8 ; - sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 22 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the upstream chemical entity" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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:deprecated ] ; - sh:targetClass biolink:ComplexMolecularMixture . - -biolink:ConceptCountAnalysisResult a sh:NodeShape ; - rdfs:subClassOf biolink:StudyResult ; - sh:closed true ; - sh:description "A result of a concept count analysis." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:path biolink:subject_closure ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical." ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path biolink:catalyst_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold 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:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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 14 ; - sh:path biolink:has_attribute ], + sh:order 19 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:order 9 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the downstream chemical entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:description "Used to hold the object 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 18 ; + sh:path biolink:subject_category ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; + sh:order 38 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "used to 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:Literal ; - sh:order 0 ; - sh:path biolink:license ], + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:ConceptCountAnalysisResult . + sh:description "used to 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:targetClass biolink:ChemicalToChemicalDerivationAssociation . -biolink:ConfidenceLevel a sh:NodeShape ; - rdfs:subClassOf biolink:InformationContentEntity ; +biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; - sh:description "Level of confidence in a statement" ; + 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:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 8 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; + sh:description "An intermediate aggregator resource 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:category ], + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "used to 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:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; + sh:order 37 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; + sh:description "Used to hold 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:Literal ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 24 ; + 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 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:ConfidenceLevel . - -biolink:ContributorAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - 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:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:boolean ; + 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:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ 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:order 23 ; + 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 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 36 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - 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 19 ; + sh:path biolink:subject_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is 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:order 18 ; + 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:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; sh:order 20 ; 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:datatype xsd:string ; + sh:description "Used to hold the object 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 "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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:datatype xsd:string ; sh:description "used to 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:Literal ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:class biolink:Agent ; - sh:description "agent helping to realise the given entity (e.g. such as a publication)" ; + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the 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:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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:DiseaseOrPhenotypicFeature ; + sh:description "the disease or phenotype that is affected by the chemical" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 35 ; + 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 17 ; + 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:nodeKind sh:Literal ; sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'" ; + sh:path biolink:iri ] ; + sh:targetClass biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation . + +biolink:ChemicalToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:description "An interaction between a chemical entity and another entity" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh: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:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - 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:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ] ; + sh:targetClass biolink:ChemicalToEntityAssociationMixin . + +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:datatype xsd:string ; + sh:description "A unique identifier 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: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:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - 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 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 4 ; + sh:path biolink: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:nodeKind sh:Literal ; sh:order 15 ; 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 22 ; - 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 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "used to 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:Literal ; sh:order 16 ; 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:datatype xsd:string ; - 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 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - 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 27 ; - sh:path biolink:retrieval_source_ids ] ; - sh:targetClass biolink:ContributorAssociation . - -biolink:CorrelatedGeneToDiseaseAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:GeneToDiseaseAssociation ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is shown to correlate with the disease." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:anyURI ; - 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 12 ; + sh:path biolink:agent_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:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - 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 33 ; + 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 32 ; + sh:path biolink:category ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical entity that is affecting the pathway" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject 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:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:qualifier ], + sh:order 28 ; + sh:path biolink:p_value ], + [ 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:datatype xsd:string ; - sh:description "used to 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:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - 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 biolink class/category 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:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; + sh:description "Used to hold the 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:original_object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], + sh:path biolink:subject_closure ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; + sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:category ], - [ 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: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:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:double ; + sh:description "An intermediate aggregator resource 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:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; + sh:order 13 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; + sh:description "Used to hold 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: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:path biolink:subject_namespace ], + [ sh:class biolink:Pathway ; + sh:description "the pathway that is affected by the chemical" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - 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 9 ; - sh:path biolink:publications ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 27 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_total ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 14 ; + 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 25 ; + sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ 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 1 ; + sh:path rdf:predicate ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 31 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - 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:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:Attribute ; + sh:order 34 ; + 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 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ] ; + 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:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 39 ; + sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; + sh:order 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:sex_qualifier ], - [ sh:datatype ; - 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:Literal ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_count ], + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:subject_closure ], + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - 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 0 ; + sh:path biolink:license ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:datatype xsd:string ; - 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 4 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; + sh:order 6 ; + 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 "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "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 "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:boolean ; + sh:order 9 ; + sh:path biolink:iri ] ; + 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:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; + sh:order 14 ; sh:path biolink:deprecated ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 36 ; + sh:order 11 ; 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:class biolink:RetrievalSource ; - sh:description "A list of 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:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ] ; - sh:targetClass biolink:CorrelatedGeneToDiseaseAssociation . - -biolink:DatasetSummary a sh:NodeShape ; - rdfs:subClassOf biolink:InformationContentEntity ; - sh:closed true ; - sh:description "an item that holds summary level information about a dataset." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 10 ; + sh:order 5 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:format ], + 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:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:nodeKind sh:Literal ; sh:order 0 ; - sh:path biolink:source_web_page ], - [ sh:datatype xsd:string ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:license ], + 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 16 ; + sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; + [ sh:description "Alternate human-readable names for a thing" ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ] ; + 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:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 8 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path schema1:logo ], + 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. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - 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 0 ; + sh:path biolink:provided_by ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; + sh:order 9 ; sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:rights ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 12 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:path biolink:deprecated ] ; + 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:datatype xsd:string ; + sh:order 9 ; sh:path rdf:type ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + [ sh:description "Alternate human-readable names for a thing" ; sh:order 5 ; - sh:path biolink:creation_date ], + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:DatasetSummary . - -biolink:DatasetVersion a sh:NodeShape ; - rdfs:subClassOf biolink:InformationContentEntity ; - sh:closed true ; - sh:description "an item that holds version level information about a dataset." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:DatasetDistribution ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path dct:distribution ], - [ sh:datatype xsd:string ; + sh:path biolink:provided_by ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:rights ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; + sh:path biolink:full_name ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:ingest_date ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:class biolink:ClinicalAttribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; sh:order 12 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 13 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:license ], + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 11 ; + sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Dataset ; - sh:maxCount 1 ; + [ 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:has_dataset ], - [ 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:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + 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:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:format ] ; - sh:targetClass biolink:DatasetVersion . + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_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:ClinicalFinding . -biolink:DiagnosticAid a sh:NodeShape ; - rdfs:subClassOf biolink:NamedThing ; +biolink:ClinicalIntervention 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:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; sh:order 7 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:minCount 1 ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 9 ; 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:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; sh:order 6 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 4 ; - sh:path biolink:id ] ; - sh:targetClass biolink:DiagnosticAid . + sh:path biolink:category ] ; + sh:targetClass biolink:ClinicalIntervention . -biolink:DiseaseOrPhenotypicFeatureExposure a sh:NodeShape ; - rdfs:subClassOf biolink:Attribute ; +biolink:ClinicalMeasurement 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: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:datatype xsd:string ; - sh:nodeKind sh:Literal ; + 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:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ 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:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 human-readable description of an entity" ; + sh:maxCount 1 ; sh:order 12 ; - sh:path rdf:type ], + 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:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 6 ; + sh:order 5 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; + sh:order 1 ; sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:string ; + 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:order 13 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; + sh:order 10 ; + sh:path biolink:category ] ; + 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:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:datatype xsd:string ; sh:order 11 ; + 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 10 ; sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; + sh:order 14 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - 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: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:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; sh:order 13 ; + sh:path biolink:has_attribute ], + [ 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 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 "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; + 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 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ] ; + 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:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:full_name ], + sh:path dct:description ], [ sh:datatype xsd:string ; - 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:Literal ; - sh:order 1 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:DiseaseOrPhenotypicFeatureExposure . - -biolink:DiseaseOrPhenotypicFeatureOutcome a sh:NodeShape ; - sh:closed true ; - sh:description "Physiological outcomes resulting from an exposure event which is the manifestation of a disease or other characteristic phenotype." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:DiseaseOrPhenotypicFeatureOutcome . - -biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 rdf:object ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 rdf:subject ] ; - sh:targetClass biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin . + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path rdf:type ] ; + sh:targetClass biolink:ClinicalTrial . -biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; +biolink:CodingSequence 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:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; + 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:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 7 ; + sh:path biolink:id ], + [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ 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`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:in_taxon_label ], + [ 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:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + 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:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 8 ; + sh:path biolink: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:description "Alternate human-readable names for a thing" ; sh:order 6 ; - sh:path biolink:publications ], + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; + sh:order 14 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 10 ; + sh:path rdf:type ] ; + sh:targetClass biolink:CodingSequence . + +biolink:Cohort a sh:NodeShape ; + sh:closed true ; + sh:description "A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that samples a cohort, performing a cross-section at intervals through time." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; - sh:order 36 ; + sh:order 12 ; 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 biolink:in_taxon_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:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; + sh:order 9 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + sh:path dct:description ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + 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 3 ; - sh:path biolink:negated ], + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:GeneticInheritance ; - sh:description "genetic inheritance associated with the specified disease or phenotypic feature." ; + sh:description "A unique 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 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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 "The value in this node property represents the knowledge provider that created or assembled the node 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: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 "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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 0 ; + sh:path biolink:license ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - 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 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:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A unique 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:Literal ; - sh:order 30 ; + sh:order 8 ; sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of 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:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the 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 name for an attribute or entity." ; + 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 22 ; - sh:path biolink:object_category_closure ], + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:qualifier ], + 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:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ] ; - sh:targetClass biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . + sh:order 15 ; + sh:path biolink:deprecated ] ; + sh:targetClass biolink:CommonDataElement . -biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; +biolink:ComplexChemicalExposure 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: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:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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 "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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:order 4 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + 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 36 ; + sh:order 13 ; 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:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "A unique identifier 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 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + 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:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; + 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. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:anyURI ; - 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:deprecated ] ; + 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:datatype xsd:string ; + sh:description "" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "used to 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 0 ; + sh:path biolink:is_supplement ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 14 ; - sh:path biolink:original_subject ], + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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: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:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 12 ; + sh:path biolink:synonym ], + [ 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, 'clinical approval status.'" ; + 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 1 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:datatype xsd:string ; + 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 human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 18 ; - 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: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: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:qualifiers ], + 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 19 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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 "" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "used to 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 biolink:trade_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 20 ; + sh:path biolink:deprecated ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:is_toxic ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + 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: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 22 ; - sh:path biolink:object_category_closure ], + sh:path biolink:routes_of_delivery ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 13 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 16 ; + sh:path rdf:type ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ] ; + 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:datatype xsd:string ; 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 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:id ], + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 2 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], + sh:order 1 ; + sh:path biolink:rights ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ 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 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 13 ; sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 11 ; + 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:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; + sh:order 11 ; sh:path rdf:type ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:path dct:description ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "anatomical entity in which the disease or feature is found." ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path rdf:object ], + sh:path biolink:format ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - 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:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Publication ; - sh:description "One or more 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:order 0 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 0 ; - sh:path rdf:subject ] ; - sh:targetClass biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:creation_date ] ; + sh:targetClass biolink:ConfidenceLevel . -biolink:DiseaseToEntityAssociationMixin a sh:NodeShape ; - sh:closed false ; +biolink:ContributorAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Any association between an entity (such as a publication) and various agents that contribute to its realisation" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink: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:property [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier 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:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:Disease ; - sh:description "disease class" ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:predicate ] ; - sh:targetClass biolink:DiseaseToEntityAssociationMixin . - -biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - sh:closed true ; - sh:description "An association between an exposure event and a disease." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource 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:datatype xsd:string ; sh:description "Used to hold 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:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ 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:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 34 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + 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:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:deprecated ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:class biolink:InformationContentEntity ; + sh:description "information content entity which an agent has helped realise" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the 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:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 36 ; - 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 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + 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 27 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - 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 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:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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 28 ; + sh:path biolink:p_value ], + [ 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:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - 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:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_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:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + 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 21 ; sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - 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 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - 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 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:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ 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 5 ; + sh:path biolink:qualifiers ], + [ 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:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + 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:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], + sh:order 31 ; + 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 32 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; 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:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Disease ; - sh:description "disease class" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:path biolink:timepoint ] ; + sh:targetClass biolink:ContributorAssociation . + +biolink:CorrelatedGeneToDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 10 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; + sh:order 6 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:description "Used to hold the subject 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_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ] ; - sh:targetClass biolink:DiseaseToExposureEventAssociation . - -biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - sh:closed true ; - sh:description "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; + sh:order 23 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 34 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:path biolink:iri ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_namespace ], + sh:order 32 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 39 ; + sh:order 36 ; sh:path rdf:type ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:knowledge_level ], - [ 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:class biolink:Publication ; + sh:description "One or more 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 biolink:onset_qualifier ], + sh:order 9 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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 46 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - 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 27 ; - 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 28 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 40 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:qualifier ], + sh:order 42 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 44 ; + 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:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink: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 8 ; + sh:path biolink:qualifiers ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:order 37 ; + 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 24 ; - sh:path biolink:object_category ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_direction_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 16 ; + sh:order 13 ; sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 36 ; - sh:path biolink:id ], - [ sh:datatype xsd:time ; - 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:nodeKind sh:Literal ; sh:order 19 ; - sh:path biolink:timepoint ], + sh:path biolink:original_object ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 42 ; + sh:order 39 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:order 43 ; + sh:path biolink:has_quotient ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is 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:order 20 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold 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:Literal ; - sh:order 9 ; - sh:path biolink:negated ], - [ 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 27 ; + sh:path biolink:object_namespace ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path rdf:object ], + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], + sh:minCount 1 ; + sh:order 33 ; + sh:path biolink:id ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 32 ; + sh:order 29 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 20 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:knowledge_source ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:p_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:order 35 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path rdfs:label ], - [ sh:class biolink:Disease ; - sh:description "disease class" ; + sh:path biolink: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:IRI ; - sh:order 5 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - 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:description "Used to hold 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:Literal ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:anyURI ; - 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:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - 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:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:publications ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; + sh:order 41 ; sh:path biolink:has_count ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + [ sh:datatype xsd:string ; + 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:nodeKind sh:Literal ; - sh:order 2 ; - 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 33 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:double ; + sh:order 47 ; + sh:path biolink:qualified_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:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:has_quotient ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 18 ; + 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:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:sex_qualifier ], + sh:order 48 ; + sh:path biolink:frequency_qualifier ], [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 18 ; - sh:path biolink:agent_type ], + sh:order 14 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:original_object ], + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path rdf:predicate ], + sh:order 11 ; + 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 30 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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 "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_namespace ], + sh:order 7 ; + sh:path biolink: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 21 ; + sh:path biolink:object_category ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path dct:description ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "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 3 ; + sh:path biolink:subject_aspect_qualifier ] ; + 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 "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:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; + sh:order 17 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path dct:description ], - [ sh:datatype ; - 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:Literal ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:iri ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ] ; - sh:targetClass biolink:DiseaseToPhenotypicFeatureAssociation . - -biolink:DrugLabel a sh:NodeShape ; - rdfs:subClassOf biolink:Publication ; - 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:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:keywords ], + sh:order 4 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:pages ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:provided_by ], - [ 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:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:minCount 1 ; + sh:order 10 ; + 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 12 ; + sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:deprecated ], + sh:order 15 ; + sh:path dct:description ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; + sh:order 5 ; sh:path biolink:creation_date ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 16 ; - sh:path biolink:category ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path schema1:logo ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:license ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:mesh_terms ], + sh:path biolink:xref ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path biolink:summary ], + sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 dct:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], + sh:order 0 ; + sh:path biolink:source_web_page ], + [ 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:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:path rdf:type ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ] ; + 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:datatype xsd:string ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path dct:description ], + sh:order 3 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; + sh:order 17 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:format ], + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 5 ; + sh:path biolink:format ], + [ sh:class biolink:DatasetDistribution ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - 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: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 "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:DrugLabel . - -biolink:DrugToEntityAssociationMixin a sh:NodeShape ; - rdfs:subClassOf biolink:ChemicalEntityToEntityAssociationMixin ; - sh:closed false ; - sh:description "An interaction between a drug and another entity" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Drug ; - sh:description "the drug that is an interactor" ; + sh:order 16 ; + sh:path dct:description ], + [ sh:class biolink:Dataset ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path rdf:subject ], + sh:path biolink:has_dataset ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:rights ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - 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:Literal ; sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:path biolink:ingest_date ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A unique 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:targetClass biolink:DrugToEntityAssociationMixin . + sh:order 11 ; + sh:path biolink:id ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:order 14 ; + sh:path rdf:type ], + [ sh:datatype xsd:date ; + 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:targetClass biolink:DatasetVersion . -biolink:DrugToGeneAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; +biolink:DiagnosticAid a sh:NodeShape ; sh:closed true ; - sh:description "An interaction between a drug and a gene or gene product." ; + sh:description "A device or substance used to help diagnose disease or injury" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; 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: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 "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + 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 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - 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 0 ; + sh:path biolink:provided_by ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; + sh:order 8 ; sh:path rdfs:label ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:anyURI ; - 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 11 ; + sh:path biolink:deprecated ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 9 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 30 ; + sh:order 4 ; sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ] ; + 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 "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; + sh:order 5 ; sh:path biolink:iri ], - [ sh:class biolink:Drug ; - sh:description "the drug that is an interactor" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier 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 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 4 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; + sh:order 12 ; sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - 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 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 36 ; + sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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 dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:description "The 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:Literal ; + 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:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:path biolink:has_quantitative_value ] ; + sh:targetClass biolink:DiseaseOrPhenotypicFeatureExposure . + +biolink:DiseaseOrPhenotypicFeatureOutcome a sh:NodeShape ; + sh:closed true ; + sh:description "Physiological outcomes resulting from an exposure event which is the manifestation of a disease or other characteristic phenotype." ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:DiseaseOrPhenotypicFeatureOutcome . + +biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ 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 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 2 ; + 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:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ] ; + sh:targetClass biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin . + +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:datatype xsd:string ; + sh:description "Used to hold the 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 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:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "used to 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:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the gene or gene product that is affected by the drug" ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + 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 27 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "used to 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 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:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - 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:timepoint ], + [ sh:class biolink:GeneticInheritance ; + sh:description "genetic inheritance associated with the specified disease or phenotypic feature." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is 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:targetClass biolink:DrugToGeneAssociation . - -biolink:DrugToGeneInteractionExposure a sh:NodeShape ; - rdfs:subClassOf biolink:DrugExposure ; - 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:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 12 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + 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 15 ; - sh:path biolink:has_attribute ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - 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 object 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:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:id ], + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:xref ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 30 ; + 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 4 ; - sh:path biolink:has_attribute_type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:has_qualitative_value ], + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + 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:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:provided_by ], + sh:description "used to 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 31 ; + sh:path biolink:iri ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - 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 "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path rdfs:label ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an 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:nodeKind sh:Literal ; sh:order 14 ; - sh:path dct:description ], + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdf:type ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ], + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 10 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:minCount 1 ; sh:order 1 ; - sh:path biolink:timepoint ], + 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:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; + sh:order 37 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:DrugToGeneInteractionExposure . + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ] ; + sh:targetClass biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . -biolink:DruggableGeneToDiseaseAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:GeneToDiseaseAssociation ; +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:RetrievalSource ; - sh:description "A list of 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 30 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold 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:Literal ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 23 ; + 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:nodeKind sh:Literal ; - sh:order 37 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:double ; + sh:description "Used to hold 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:Literal ; - sh:order 43 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_percentage ], + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - 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:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:qualified_predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; - sh:order 4 ; - 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:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:iri ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular 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:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_count ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the 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 ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_label_closure ], + sh:order 21 ; + 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 7 ; + sh:path biolink:has_evidence ], [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:description "connects an association to an instance of supporting evidence" ; - sh:in ( "tclin" "tbio" "tchem" "tdark" ) ; - sh:order 10 ; - sh:path biolink:has_evidence ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:description "Used to hold the 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 "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 26 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:path biolink: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:Literal ; + sh:nodeKind sh:IRI ; sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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 14 ; - sh:path biolink:knowledge_level ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; + sh:order 37 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdf:type ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "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 subject 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 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:subject_aspect_qualifier ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; + sh:order 20 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:datatype xsd:anyURI ; - 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 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:nodeKind sh:IRI ; sh:order 18 ; - sh:path biolink:original_predicate ], + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object 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:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "anatomical entity in which the disease or feature is found." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 25 ; + sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; + sh:order 13 ; sh:path biolink:timepoint ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - 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 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "used to 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:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + 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:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; + sh:order 28 ; sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - 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 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:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:minCount 1 ; sh:order 12 ; - 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:path biolink:agent_type ] ; + sh:targetClass biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . + +biolink:DiseaseToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Disease ; + sh:description "disease class" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:Publication ; - sh:description "One or more 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:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; + [ 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: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:datatype xsd:string ; + sh:description "Used to hold the object 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:datatype xsd:boolean ; + 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:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; sh:order 28 ; - sh:path biolink:subject_label_closure ], + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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 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:Literal ; - sh:order 27 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:knowledge_source ], + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 33 ; + sh:order 30 ; 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 "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:class biolink:RetrievalSource ; + sh:description "A list of 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: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 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold 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 21 ; - sh:path biolink:object_category ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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 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:has_attribute ], + sh:order 22 ; + 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 31 ; + 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:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:qualifier ] ; - sh:targetClass biolink:DruggableGeneToDiseaseAssociation . - -biolink:EntityToDiseaseAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ 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 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Disease ; + sh:description "disease class" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 19 ; + sh:order 17 ; 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:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - 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 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + 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 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "used to 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: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:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ 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:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is 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:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; + sh:order 12 ; sh:path biolink:agent_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 8 ; + sh:order 6 ; sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; + 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:negated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:p_value ], + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold 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:Literal ; - sh:order 37 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], + 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:description "Used to hold the 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:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:qualifier ], + sh:order 4 ; + sh:path biolink:qualifier ] ; + sh:targetClass biolink:DiseaseToExposureEventAssociation . + +biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:iri ], + sh:order 15 ; + 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 12 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object 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_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 0 ; + sh:path biolink:onset_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; + sh:order 32 ; 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 33 ; + 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 23 ; + 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 38 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; + sh:order 43 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 11 ; - 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 23 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ 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:Literal ; - sh:order 3 ; + sh:order 6 ; sh:path rdf:predicate ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - 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:order 29 ; + sh:path biolink:subject_namespace ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 44 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], + sh:order 2 ; + sh:path biolink:has_total ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 42 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; + sh:order 25 ; sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; + sh:description "used to 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 22 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:description "" ; - sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 39 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 16 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:clinical_approval_status ], - [ sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_2" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:order 1 ; - sh:path biolink:max_research_phase ], + sh:path biolink:has_count ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:iri ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:has_quotient ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path dct:description ], + [ sh:class biolink:Disease ; + sh:description "disease class" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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 "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + 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 48 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 32 ; + sh:order 36 ; 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 24 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 35 ; + sh:path biolink:adjusted_p_value ], + [ 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:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "used to 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 49 ; + sh:path biolink:frequency_qualifier ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - 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 29 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:anyURI ; - 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 18 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:boolean ; + 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:negated ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:minCount 1 ; sh:order 17 ; - sh:path biolink:original_predicate ], + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:has_percentage ], [ 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:targetClass biolink:EntityToDiseaseAssociation . - -biolink:EntityToDiseaseAssociationMixin a sh:NodeShape ; - rdfs:subClassOf biolink:EntityToFeatureOrDiseaseQualifiersMixin ; - 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 "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_direction_qualifier ], - [ 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:order 13 ; + 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 6 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype ; - 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:Literal ; - sh:order 5 ; - sh:path biolink:frequency_qualifier ], + sh:order 11 ; + sh:path biolink:qualifiers ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 3 ; + sh:order 47 ; sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:object_category ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; - 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:description "Used to hold the subject 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:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:order 14 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to 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 20 ; + 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 8 ; - sh:path rdf:object ], + sh:order 28 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - 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:order 30 ; + 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 21 ; + sh:path biolink:original_predicate ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 19 ; + sh:path biolink:timepoint ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; + sh:nodeKind sh:IRI ; sh:order 7 ; - sh:path rdf:predicate ] ; - sh:targetClass biolink:EntityToDiseaseAssociationMixin . + sh:path rdf:object ] ; + sh:targetClass biolink:DiseaseToPhenotypicFeatureAssociation . -biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin a sh:NodeShape ; - sh:closed false ; +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:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + sh:property [ sh:datatype xsd:string ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:minCount 1 ; + sh:order 13 ; + sh:path dct:description ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 1 ; + sh:path biolink:has_quantitative_value ], + [ 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 8 ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 1 ; - sh:path rdf:predicate ] ; - sh:targetClass biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin . - -biolink:EntityToExposureEventAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:description "An association between some entity and an exposure event." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ 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 11 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_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 2 ; - sh:path rdf:object ], + 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:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 4 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ] ; - sh:targetClass biolink:EntityToExposureEventAssociationMixin . + sh:order 6 ; + sh:path biolink:id ] ; + sh:targetClass biolink:DrugExposure . -biolink:EntityToOutcomeAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:description "An association between some entity and an outcome" ; +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: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:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 21 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 19 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - 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:Literal ; - sh:order 1 ; - sh:path rdf:predicate ] ; - sh:targetClass biolink:EntityToOutcomeAssociationMixin . - -biolink:EntityToPhenotypicFeatureAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_2" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:max_research_phase ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of 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 8 ; + 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 29 ; - sh:path biolink:retrieval_source_ids ], + sh:order 20 ; + 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:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:path biolink:license ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 10 ; + 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:nodeKind sh:Literal ; - sh:order 36 ; + sh:order 15 ; + sh:path biolink:iri ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:order 18 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:subject_closure ], + sh:order 17 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:order 6 ; + sh:path dct:type ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + 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:nodeKind sh:Literal ; + sh:order 14 ; + 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:datatype xsd:string ; + sh:description "keywords tagging a publication" ; sh:order 3 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:deprecated ], + sh:path biolink:keywords ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:iri ], + sh:order 9 ; + 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 16 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "used to 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 "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:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the 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:OntologyClass ; - sh:description "Used to hold the 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 biolink:summary ] ; + sh:targetClass biolink:DrugLabel . + +biolink:DrugToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:description "An interaction between a drug and another entity" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:category ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh: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:subject ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 17 ; - 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 9 ; - sh:path biolink:has_evidence ], - [ 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:path rdf:object ], + [ sh:class biolink:Drug ; + sh:description "the drug that is an interactor" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 0 ; + sh:path rdf:subject ] ; + sh:targetClass biolink:DrugToEntityAssociationMixin . + +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:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 30 ; - sh:path biolink:p_value ], + 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:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 38 ; + sh:order 36 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_label_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the 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:Drug ; + sh:description "the drug that is an interactor" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "used to 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:Literal ; - sh:order 18 ; + sh:order 16 ; sh:path biolink:original_object ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; + sh:description "Used to hold the object 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:RetrievalSource ; + sh:description "A list of 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:subject_label_closure ], - [ sh:description "" ; - sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:clinical_approval_status ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + 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:Literal ; - sh:order 5 ; - sh:path biolink:negated ], + 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:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_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:order 32 ; - 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 24 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:object_closure ], + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - 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 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the gene or gene product that is affected by the drug" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + 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 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; + sh:order 4 ; sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 26 ; - sh:path biolink:object_namespace ] ; - sh:targetClass biolink:EntityToPhenotypicFeatureAssociation . - -biolink:EntityToPhenotypicFeatureAssociationMixin a sh:NodeShape ; - rdfs:subClassOf biolink:EntityToFeatureOrDiseaseQualifiersMixin ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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:object_direction_qualifier ], - [ 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 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:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "used to 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:Literal ; - sh:order 8 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:has_total ], + sh:order 34 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - 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 namespace of 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:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:boolean ; + 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:subject_direction_qualifier ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:double ; + sh:path biolink:timepoint ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:has_quotient ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 35 ; + 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 15 ; + 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 3 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:has_count ], - [ 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 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:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ] ; - sh:targetClass biolink:EntityToPhenotypicFeatureAssociationMixin . - -biolink:EnvironmentalFeature a sh:NodeShape ; - rdfs:subClassOf biolink:PlanetaryEntity ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 4 ; + sh:order 30 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - 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 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 7 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or 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 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold 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:Literal ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ] ; - sh:targetClass biolink:EnvironmentalFeature . + sh:order 24 ; + sh:path biolink:object_namespace ] ; + sh:targetClass biolink:DrugToGeneAssociation . -biolink:EnvironmentalFoodContaminant a sh:NodeShape ; - rdfs:subClassOf biolink:ChemicalEntity ; +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:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 1 ; - sh:path biolink:available_from ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_attribute_type ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; + sh:nodeKind sh:IRI ; sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:path biolink:has_qualitative_value ], + [ 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:trade_name ], - [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:path biolink:has_gene_or_gene_product ], + [ 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 point in time" ; + sh:maxCount 1 ; + sh:order 1 ; + 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:nodeKind sh:Literal ; sh:order 3 ; - sh:path biolink:is_toxic ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + 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 12 ; + sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path dct:description ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path biolink:iri ], + sh:path biolink:full_name ], [ 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:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - 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:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; - sh:path biolink:max_tolerated_dose ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 9 ; - sh:path biolink:id ], + sh:path biolink:has_quantitative_value ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 11 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:EnvironmentalFoodContaminant . - -biolink:EnvironmentalProcess a sh:NodeShape ; - rdfs:subClassOf biolink:PlanetaryEntity ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; + sh:order 8 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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 10 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:EnvironmentalProcess . + sh:order 7 ; + sh:path biolink:id ] ; + sh:targetClass biolink:DrugToGeneInteractionExposure . -biolink:EpidemiologicalOutcome a sh:NodeShape ; +biolink:DruggableGeneToDiseaseAssociation a sh:NodeShape ; sh:closed true ; - sh:description "An epidemiological outcome, such as societal disease burden, resulting from an exposure event." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:EpidemiologicalOutcome . - -biolink:EpigenomicEntity a sh:NodeShape ; - sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; + sh:property [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ] ; - sh:targetClass biolink:EpigenomicEntity . - -biolink:Event a sh:NodeShape ; - rdfs:subClassOf biolink:NamedThing ; - sh:closed true ; - sh:description "Something that happens at a given place and time." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 44 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 3 ; + sh:path biolink:subject_aspect_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:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:xref ], + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 4 ; + sh:order 33 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ], + sh:order 6 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + 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:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], + sh:order 47 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:Event . - -biolink:ExonToTranscriptRelationship a sh:NodeShape ; - rdfs:subClassOf biolink:SequenceFeatureRelationship ; - sh:closed true ; - sh:description "A transcript is formed from multiple exons" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; + sh:order 23 ; 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 25 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject 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_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; + sh:order 7 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 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:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], + sh:order 16 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - 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 6 ; - sh:path biolink:publications ], + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "used to 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:Literal ; - sh:order 14 ; + sh:order 17 ; sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 30 ; - 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:order 34 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 36 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ 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:order 8 ; + sh:path biolink:qualifiers ], + [ 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: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:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], + sh:order 15 ; + sh:path biolink:agent_type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; + sh:order 24 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:double ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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 43 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; + sh:order 32 ; sh:path biolink:adjusted_p_value ], - [ 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:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], + sh:order 38 ; + sh:path dct:description ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path rdfs:label ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:has_count ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; + sh:order 28 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 35 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category 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 11 ; - sh:path biolink:knowledge_level ], - [ 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:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 20 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:order 31 ; + sh:path biolink:p_value ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 36 ; + sh:order 39 ; 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:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ] ; - sh:targetClass biolink:ExonToTranscriptRelationship . - -biolink:ExposureEventToOutcomeAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - sh:closed true ; - sh:description "An association between an exposure event and an outcome." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 26 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 16 ; - 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:description "Used to hold the object label 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:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - 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:description "used to 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 19 ; - 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 24 ; - sh:path biolink:object_category_closure ], + sh:path biolink:original_object ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; + sh:order 14 ; sh:path biolink:knowledge_level ], - [ 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:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 13 ; + 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:nodeKind sh:Literal ; sh:order 18 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:negated ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 42 ; + 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:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:deprecated ], - [ 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:order 48 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "connects an association to an instance of supporting evidence" ; + sh:in ( "tclin" "tbio" "tchem" "tdark" ) ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; sh:order 4 ; - sh:path rdf:object ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdf:type ], + sh:order 40 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Used to hold 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:Literal ; - sh:order 25 ; + sh:order 26 ; sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; + sh:order 11 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path dct:description ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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 38 ; - 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 23 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is 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:order 21 ; sh:path biolink:object_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold 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: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 9 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:path biolink:publications ] ; + 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: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:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; + sh:order 1 ; + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:deprecated ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 3 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:time ; - sh:description "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier." ; + sh:order 0 ; + sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:temporal_context_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:Publication ; - sh:description "One or more 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 4 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 3 ; + sh:path rdf:type ] ; + sh:targetClass biolink:Entity . + +biolink:EntityToDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ 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:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; sh:order 32 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 34 ; + sh:path biolink:category ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:iri ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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 14 ; - sh:path biolink:agent_type ], + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - 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:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_2" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:max_research_phase ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 35 ; + 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 2 ; - sh:path rdf:subject ] ; - sh:targetClass biolink:ExposureEventToOutcomeAssociation . - -biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - 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:datatype xsd:string ; + sh:order 7 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; + sh:order 22 ; sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold 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:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 26 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; + sh:order 27 ; sh:path biolink:subject_label_closure ], - [ sh:datatype ; - 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:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], + sh:order 36 ; + sh:path rdfs:label ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:publications ], + [ sh: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 "" ; + sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:clinical_approval_status ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "used to 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:Literal ; - sh:order 43 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 18 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - 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:description "An intermediate aggregator resource 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 point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:anyURI ; - 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 39 ; + sh:path biolink:deprecated ], + [ 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 3 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:boolean ; + 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:datatype xsd:string ; + sh:description "used to 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:Literal ; sh:order 16 ; - sh:path biolink:original_predicate ], + 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:description "Used to hold the biolink class/category of an association. This is 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:qualifiers ], + sh:order 20 ; + 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 23 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object 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:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; + sh:order 31 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ 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:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:timepoint ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + 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 23 ; + sh:order 24 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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 28 ; + sh:order 29 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_object ], + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - 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 25 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; + sh:order 21 ; 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 18 ; + sh:order 19 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:double ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_quotient ], - [ 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 30 ; + sh:path biolink:p_value ] ; + 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 "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; + sh:order 8 ; sh:path rdf:object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ 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:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + 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 4 ; + sh:path biolink:qualified_predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:ExposureEvent ; + sh:order 1 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:object_aspect_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:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:frequency_qualifier ] ; + sh:targetClass biolink:EntityToDiseaseAssociationMixin . + +biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh: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:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ 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:EntityToDiseaseOrPhenotypicFeatureAssociationMixin . + +biolink:EntityToExposureEventAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:description "An association between some entity and an exposure event." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ 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 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:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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: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:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ] ; + sh:targetClass biolink:EntityToExposureEventAssociationMixin . + +biolink:EntityToFeatureOrDiseaseQualifiersMixin a sh:NodeShape ; + sh:closed false ; + sh:description "Qualifiers for entity to disease or phenotype associations." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink: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:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:has_count ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 2 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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 "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:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:order 4 ; + sh:path biolink:qualified_predicate ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 44 ; + sh:order 1 ; sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + [ sh: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:sex_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; + sh:order 7 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_aspect_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 5 ; + sh:path biolink:frequency_qualifier ], + [ 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 19 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 8 ; + sh:path rdf:object ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:order 3 ; + sh:path biolink:object_direction_qualifier ] ; + sh:targetClass biolink:EntityToFeatureOrDiseaseQualifiersMixin . + +biolink:EntityToOutcomeAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:description "An association between some entity and an outcome" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Outcome ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ] ; + sh:targetClass biolink:EntityToOutcomeAssociationMixin . + +biolink:EntityToPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:object_label_closure ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "used to 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 dct:description ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - 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 8 ; - 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 36 ; + 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 7 ; - sh:path biolink:publications ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 2 ; + sh:path rdf:subject ], + [ 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 13 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; + sh:order 12 ; sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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 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:datatype xsd:string ; + sh:description "used to 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:Literal ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 18 ; + 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 23 ; + 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:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 26 ; + 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 34 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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 21 ; + 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:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], + sh:order 33 ; + 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: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:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 7 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:path biolink:negated ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ] ; - sh:targetClass biolink:ExposureEventToPhenotypicFeatureAssociation . - -biolink:Food a sh:NodeShape ; - rdfs:subClassOf biolink:ChemicalMixture ; - sh:closed true ; - sh:description "A substance consumed by a living organism as a source of nutrition" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 15 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ 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:Literal ; - sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:minCount 1 ; sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - 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 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:synonym ], + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + 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:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 19 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:is_supplement ], + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdfs:label ], + sh:order 25 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:trade_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, 'clinical approval status.'" ; - 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:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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:highest_FDA_approval_status ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:description "" ; + sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path dct:description ], + sh:order 0 ; + sh:path biolink:clinical_approval_status ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; sh:order 11 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + 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 24 ; + sh:path biolink:object_category_closure ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - 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:order 15 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], + sh:order 30 ; + sh:path biolink:p_value ], + [ 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:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdf:type ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ] ; - sh:targetClass biolink:Food . - -biolink:FoodAdditive a sh:NodeShape ; - rdfs:subClassOf biolink:ChemicalEntity ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "used to 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:Literal ; sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:path biolink:original_subject ], + [ sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_2" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - 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:order 1 ; + sh:path biolink:max_research_phase ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 9 ; + sh:order 32 ; sh:path biolink:id ], - [ 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 15 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 31 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:is_toxic ], + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 35 ; + 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 8 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:trade_name ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 6 ; + sh:path biolink: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 29 ; + sh:path biolink:retrieval_source_ids ] ; + sh:targetClass biolink:EntityToPhenotypicFeatureAssociation . + +biolink:EntityToPhenotypicFeatureAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + 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:Literal ; - sh:order 7 ; - sh:path biolink:full_name ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - 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 "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:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:max_tolerated_dose ] ; - sh:targetClass biolink:FoodAdditive . - -biolink:FrequencyQuantifier a sh:NodeShape ; - rdfs:subClassOf biolink:RelationshipQuantifier ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:double ; + sh:order 12 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:has_quotient ], + sh:order 7 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:integer ; sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; + sh:order 5 ; sh:path biolink:has_total ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:has_percentage ], + sh:order 9 ; + sh:path biolink:subject_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 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:has_count ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:has_quotient ], + [ 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 2 ; + sh:path rdf:object ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:has_count ] ; - sh:targetClass biolink:FrequencyQuantifier . + sh:path rdf:subject ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:object_direction_qualifier ] ; + sh:targetClass biolink:EntityToPhenotypicFeatureAssociationMixin . -biolink:Fungus a sh:NodeShape ; - rdfs:subClassOf biolink:CellularOrganism ; +biolink:EnvironmentalExposure 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: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:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - 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 14 ; + sh:path biolink:has_attribute ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; + sh:order 9 ; 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: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:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 15 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 10 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + 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:nodeKind sh:Literal ; - sh:order 7 ; + sh:order 5 ; sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; + [ sh:description "a point in time" ; + sh:maxCount 1 ; sh:order 0 ; - sh:path biolink:in_taxon ], + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - 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 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 "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + 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:nodeKind sh:Literal ; - sh:order 10 ; + sh:order 1 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:EnvironmentalExposure . + +biolink:EnvironmentalFeature 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 8 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; + sh:order 9 ; 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 6 ; + sh:path biolink:category ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 "may often be an organism attribute" ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 10 ; 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 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 6 ; - sh:path biolink:id ] ; - sh:targetClass biolink:Fungus . + sh:order 4 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:deprecated ] ; + sh:targetClass biolink:EnvironmentalFeature . -biolink:GeneAffectsChemicalAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; +biolink:EnvironmentalFoodContaminant a sh:NodeShape ; sh:closed true ; - sh:description "Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, activity, localization, processing, transport, etc.)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:AnatomicalEntity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:object_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to 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:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 8 ; + sh:path biolink:synonym ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:timepoint ], + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - 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 rdf:type ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:id ], + sh:order 7 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 25 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "" ; sh:maxCount 1 ; + sh:order 0 ; + 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 34 ; - sh:path biolink:object_category ], - [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; - sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; + sh:order 4 ; + sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:causal_mechanism_qualifier ], + sh:order 2 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:object_label_closure ], + sh:order 3 ; + sh:path biolink:is_toxic ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 51 ; - 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:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 31 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:description "A unique identifier 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: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 15 ; - sh:path biolink:species_context_qualifier ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 6 ; + sh:path biolink:xref ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:order 14 ; + sh:path dct:description ] ; + sh:targetClass biolink:EnvironmentalFoodContaminant . + +biolink:EnvironmentalProcess a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], + [ 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 13 ; - sh:path biolink:anatomical_context_qualifier ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "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 5 ; + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 9 ; + 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 long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:iri ], + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 49 ; + sh:order 7 ; sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 52 ; + sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 18 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:object_closure ], + sh:order 6 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:subject_derivative_qualifier ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; - 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:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "A unique identifier 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:knowledge_level ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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 4 ; + sh:path biolink:id ] ; + sh:targetClass biolink:EnvironmentalProcess . + +biolink:EpidemiologicalOutcome a sh:NodeShape ; + sh:closed true ; + sh:description "An epidemiological outcome, such as societal disease burden, resulting from an exposure event." ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:EpidemiologicalOutcome . + +biolink:EpigenomicEntity a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "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 0 ; + sh:path biolink:has_biological_sequence ] ; + sh:targetClass biolink:EpigenomicEntity . + +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:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 8 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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 rdfs:label ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:subject_namespace ], + sh:order 5 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 53 ; + sh:order 11 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - 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 rdf:type ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:subject_category ], + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdf:predicate ], - [ sh:class biolink:GeneOrGeneProduct ; - 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:id ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 16 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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 9 ; + sh:path dct:description ] ; + 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:datatype xsd:string ; + sh:description "used to 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:Literal ; - sh:order 40 ; - sh:path biolink:object_namespace ], + sh:order 14 ; + 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 22 ; + sh:order 6 ; sh:path biolink:publications ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier 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 "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:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is 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:has_evidence ], + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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: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 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 43 ; + sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:datatype xsd:string ; + sh:description "used to 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:datatype xsd:string ; + sh:description "Used to hold the subject 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 5 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; - sh:in ( "metabolite" ) ; + sh:path biolink:qualifiers ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:object_derivative_qualifier ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:order 35 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_part_qualifier ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object 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:datatype xsd:string ; + sh:description "Used to hold 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:Literal ; - sh:order 30 ; - 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:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object 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:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:object_category_closure ], + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "used to hold the original 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 name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; + sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:object_form_or_variant_qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold 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:Literal ; - sh:order 44 ; - sh:path biolink:p_value ], - [ sh:class biolink:AnatomicalEntity ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:subject_context_qualifier ], + 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:description "Used to hold the 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:qualifiers ], + 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 7 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 37 ; + sh:order 21 ; sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 28 ; + sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:category ] ; - sh:targetClass biolink:GeneAffectsChemicalAssociation . - -biolink:GeneAsAModelOfDiseaseAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:GeneToDiseaseAssociation ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The relationship to the disease" ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ 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:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + 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 32 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ] ; + sh:targetClass biolink:ExonToTranscriptRelationship . + +biolink:ExposureEventToOutcomeAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between an exposure event and an outcome." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "Used to hold 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:Literal ; - sh:order 27 ; + sh:order 26 ; sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:order 13 ; - 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 30 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:path biolink:knowledge_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 10 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 20 ; + sh:path biolink:object_category ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path dct:description ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink: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 2 ; - sh:path rdf:object ], + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object 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:RetrievalSource ; + sh:description "A list of 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:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; + sh:order 10 ; sh:path biolink:knowledge_source ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:datatype xsd:boolean ; + 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:object_direction_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 5 ; + sh:path biolink:negated ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 30 ; + sh:path biolink:p_value ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:timepoint ], + sh:order 3 ; + 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 8 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 22 ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:qualifier ], + [ 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:datatype xsd:string ; + sh:description "used to 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:datatype xsd:string ; + sh:description "Used to hold the 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:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path biolink:deprecated ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 12 ; + sh:order 11 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 34 ; + 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 7 ; + sh:path biolink:qualifiers ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], + sh:order 37 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ], + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "used to 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 22 ; + 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:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_object ], - [ 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:order 33 ; + sh:path biolink:iri ], + [ 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:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 4 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "used to 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:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 19 ; + sh:path biolink:subject_category ], + [ 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:Literal ; - sh:order 6 ; - sh:path biolink:negated ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:population_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 35 ; + 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:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_count ], + sh:order 17 ; + 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 9 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 24 ; + sh:order 23 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 33 ; - sh:path biolink:id ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_total ], [ sh:datatype xsd:string ; sh:description "Used to hold 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:Literal ; + sh:order 25 ; + sh:path biolink:subject_namespace ] ; + 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:datatype xsd:string ; + sh:description "Used to hold the subject 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_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:path biolink:subject_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 9 ; - sh:path biolink:publications ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 10 ; + 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:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:double ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; sh:order 35 ; - sh:path biolink:category ], + sh:path rdfs:label ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:iri ], + sh:order 24 ; + 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 33 ; + sh:path biolink:category ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_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 20 ; + sh:order 18 ; sh:path biolink:subject_category ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource 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 "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 44 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object 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:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_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: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:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:path biolink:has_count ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - 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 25 ; - sh:path biolink:object_category_closure ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:double ; sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; + sh:order 42 ; sh:path biolink:has_percentage ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "used to 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 "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ], + sh:order 5 ; + sh:path biolink: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 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 3 ; + sh:order 43 ; sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdfs:label ] ; - 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: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:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:phenotypic_state ], + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Optional quantitative value indicating degree of expression." ; - 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 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:order 6 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "used to 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:class biolink:OntologyClass ; + sh:description "Used to hold the 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 biolink:expression_site ], - [ sh:class biolink:LifeStage ; - sh:description "stage during which gene or protein expression of takes place." ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:stage_qualifier ] ; - sh:targetClass biolink:GeneExpressionMixin . - -biolink:GeneGroupingMixin a sh:NodeShape ; - sh:closed false ; - sh:description "any grouping of multiple genes or gene products" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ 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:GeneGroupingMixin . - -biolink:GeneHasVariantThatContributesToDiseaseAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:GeneToDiseaseAssociation ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold 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:Literal ; - sh:order 35 ; - sh:path biolink:iri ], + sh:order 25 ; + sh:path biolink:object_namespace ], + [ 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 biolink class/category of an association. This is 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:order 19 ; 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:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; + sh:order 48 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 31 ; + 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 11 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + 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 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_count ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "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 41 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:has_total ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 16 ; + sh:order 13 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ 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:Literal ; - sh:order 39 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], + sh:order 3 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:object_aspect_qualifier ], + [ 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:qualifier ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + 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:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:timepoint ], + sh:order 47 ; + sh:path biolink:qualified_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 16 ; + sh:path biolink:original_predicate ], + [ 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 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - 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 20 ; + sh:path biolink:subject_closure ] ; + sh:targetClass biolink:ExposureEventToPhenotypicFeatureAssociation . + +biolink:FeatureOrDiseaseQualifiersToEntityMixin a sh:NodeShape ; + sh:closed false ; + sh:description "Qualifiers for disease or phenotype to entity associations." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_aspect_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:nodeKind sh:Literal ; - sh:order 2 ; + sh:order 7 ; 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:maxCount 1 ; + sh:order 5 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 47 ; + sh:order 2 ; sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ 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 5 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path rdf:subject ], + [ 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:order 8 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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 "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 19 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:double ; + sh:order 3 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + 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:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 4 ; + sh:path biolink:qualified_predicate ] ; + sh:targetClass biolink:FeatureOrDiseaseQualifiersToEntityMixin . + +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:datatype xsd:string ; + sh:order 16 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 4 ; + sh:path biolink:trade_name ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ 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:order 17 ; + sh:path rdfs:label ], + [ 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, 'clinical approval status.'" ; + 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:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; sh:order 1 ; - sh:path rdf:subject ], + sh:path biolink:highest_FDA_approval_status ], + [ 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:datatype xsd:string ; - sh:description "Used to hold 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 highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - 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 10 ; - sh:path biolink:publications ], + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 7 ; - 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:path biolink:is_toxic ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:deprecated ], + [ 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 9 ; - 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: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 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:has_attribute ], + [ sh:description "Alternate human-readable names for a thing" ; sh:order 12 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to 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 biolink:synonym ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:category ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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: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:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_object ], + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 34 ; + sh:order 13 ; sh:path biolink:id ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:deprecated ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 14 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "" ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 0 ; + sh:path biolink:is_supplement ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:sex_qualifier ], + sh:order 18 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:class biolink: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 9 ; + sh:path biolink:provided_by ] ; + sh:targetClass biolink:Food . + +biolink:FoodAdditive 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 40 ; + sh:order 15 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], + 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 6 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 38 ; - 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 2 ; + sh:path biolink:max_tolerated_dose ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 11 ; + sh:path biolink:category ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], + sh:order 4 ; + sh:path biolink:has_chemical_role ], [ sh:datatype xsd:string ; - sh:description "used to 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 "" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:order 0 ; + sh:path biolink:trade_name ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 8 ; + sh:path biolink:synonym ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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 7 ; + sh:path biolink:full_name ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path biolink:primary_knowledge_source ], + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + 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 10 ; + sh:path biolink:iri ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 1 ; + sh:path biolink:available_from ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_total ] ; - sh:targetClass biolink:GeneHasVariantThatContributesToDiseaseAssociation . + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:id ] ; + sh:targetClass biolink:FoodAdditive . -biolink:GeneProductIsoformMixin a sh:NodeShape ; - rdfs:subClassOf biolink:GeneProductMixin ; +biolink:FrequencyQualifierMixin 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:description "Qualifier for frequency type associations" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; + sh:property [ 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 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - 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:path rdf:subject ], + [ 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 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:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:GeneProductIsoformMixin . + sh:path biolink:frequency_qualifier ] ; + sh:targetClass biolink:FrequencyQualifierMixin . -biolink:GeneRegulatesGeneAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; +biolink:FrequencyQuantifier a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:integer ; + 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 "Describes a regulatory relationship between two genes or gene products." ; + 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:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:property [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the 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 3 ; - sh:path biolink:species_context_qualifier ], + sh:order 22 ; + 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:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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:datatype xsd:string ; + sh:description "Used to hold the object 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:Publication ; + sh:description "One or more 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:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; + sh:order 29 ; sh:path biolink:adjusted_p_value ], + [ 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:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to 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:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], - [ sh:description "the aspect of the object gene or gene product that is being regulated, must be a descendant of \"activity_or_abundance\"\"" ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "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 16 ; + sh:path biolink:original_object ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - 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: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 "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:Literal ; - sh:order 2 ; - sh:path biolink:qualified_predicate ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:knowledge_source ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; + 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:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:order 2 ; + sh:path rdf:object ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 16 ; + sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:timepoint ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "Used to hold 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:Literal ; - sh:order 28 ; + sh:order 24 ; 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 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "used to 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:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_object ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path rdf:predicate ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 25 ; + 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:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:GeneOrGeneProduct ; - 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 36 ; + 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:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 4 ; - sh:path rdf:subject ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold 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:Literal ; - sh:order 18 ; - 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 11 ; - sh:path biolink:has_evidence ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:class biolink:RetrievalSource ; sh:description "A list of 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:order 27 ; 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 21 ; - sh:path biolink:subject_category ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 6 ; - sh:path rdf:object ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ] ; + 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:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 34 ; + sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - 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 9 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; + 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 0 ; + sh:path biolink:in_taxon ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + 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 7 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; - sh:order 40 ; + sh:order 12 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], + sh:order 1 ; + sh:path biolink:in_taxon_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:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 36 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:Fungus . + +biolink:GeneAffectsChemicalAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, activity, localization, processing, transport, etc.)" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 52 ; + 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 48 ; sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 37 ; + sh:order 49 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "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 8 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold 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:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ] ; - sh:targetClass biolink:GeneRegulatesGeneAssociation . - -biolink:GeneToEntityAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene that is the subject of the association" ; + sh:order 39 ; + sh:path biolink:subject_namespace ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 10 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 7 ; + sh:path biolink:object_part_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:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ] ; - sh:targetClass biolink:GeneToEntityAssociationMixin . - -biolink:GeneToExpressionSiteAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - 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:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 17 ; + sh:path rdf:predicate ], + [ 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:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location." ; + sh:order 13 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; sh:order 34 ; - sh:path biolink:category ], + sh:path biolink:object_category ], + [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; + sh:in ( "metabolite" ) ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:object_derivative_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 23 ; - sh:path biolink:subject_category_closure ], + sh:order 21 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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_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 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:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 37 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], + sh:order 53 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "expression relationship" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - 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 42 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - 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 7 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:species_context_qualifier ], + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:anyURI ; - 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:nodeKind sh:IRI ; + sh:order 18 ; + sh:path rdf:object ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; + sh:order 6 ; + sh:path biolink:object_form_or_variant_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + 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 31 ; 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:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], + sh:order 29 ; + sh:path biolink:timepoint ], [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which the gene is expressed" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; - sh:path rdf:object ], + sh:path biolink:subject_context_qualifier ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:order 19 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 22 ; + sh:order 36 ; sh:path biolink:object_closure ], - [ sh:class biolink:LifeStage ; - sh:description "stage at which the gene is expressed in the site" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:stage_qualifier ], - [ sh: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:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; + sh:order 50 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:id ], + sh:order 47 ; + sh:path biolink:iri ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:subject_direction_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 29 ; + sh:order 43 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "can be used to indicate magnitude, or also ranking" ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:quantifier_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:minCount 1 ; + sh:order 28 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], + sh:order 44 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - 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 41 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; + sh:order 24 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ 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:nodeKind sh:Literal ; - sh:order 37 ; + sh:order 12 ; + sh:path biolink:causal_mechanism_qualifier ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 51 ; sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:negated ], + sh:order 2 ; + sh:path biolink:subject_derivative_qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 45 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "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 3 ; + sh:path biolink:subject_aspect_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 33 ; + sh:path biolink:subject_category ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + 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:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:subject_closure ], + 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 14 ; + sh:path biolink:qualified_predicate ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; + sh:order 27 ; sh:path biolink:knowledge_level ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; + 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 "Used to hold the 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 38 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:time ; - 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:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 32 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "used to 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:Literal ; sh:order 30 ; - sh:path biolink:p_value ], + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold 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 40 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:GeneOrGeneProduct ; + 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:BlankNodeOrIRI ; + sh:order 16 ; + 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 23 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 46 ; + sh:path biolink:id ], + [ sh:class biolink:AnatomicalEntity ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:object_context_qualifier ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; + sh:order 26 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ] ; - sh:targetClass biolink:GeneToExpressionSiteAssociation . + sh:order 25 ; + sh:path biolink:primary_knowledge_source ] ; + sh:targetClass biolink:GeneAffectsChemicalAssociation . -biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:GeneToGeneAssociation ; +biolink:GeneAsAModelOfDiseaseAssociation 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:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 19 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 34 ; + sh:path biolink:iri ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:order 16 ; - sh:path biolink:agent_type ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:expression_site ], + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + 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 40 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 20 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path dct:description ], + sh:order 44 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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 "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:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 47 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "used to 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:Literal ; - sh:order 7 ; - sh:path biolink:negated ], + sh:order 17 ; + 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 25 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; + sh:order 7 ; sh:path biolink:qualifier ], - [ 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:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - 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 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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 37 ; + sh:path rdfs:label ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:category ], + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to 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 "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 36 ; + 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:nodeKind sh:Literal ; sh:order 18 ; - sh:path biolink:original_subject ], + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 34 ; - sh:path biolink:id ], - [ sh:class biolink:LifeStage ; - sh:description "stage during which gene or protein expression of takes place." ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:stage_qualifier ], + sh:order 46 ; + sh:path biolink:object_aspect_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 "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:BlankNodeOrIRI ; - sh:order 6 ; - sh:path rdf:object ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:has_total ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdf:type ], - [ 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 object 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_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:deprecated ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 4 ; - sh:path rdf:subject ], + sh:order 14 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ 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:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Optional quantitative value indicating degree of expression." ; + sh:description "An intermediate aggregator resource 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 human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path dct:description ], + [ 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:quantifier_qualifier ], + sh:order 5 ; + sh:path biolink:sex_qualifier ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 35 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "used to 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:Literal ; - sh:order 20 ; + sh:order 19 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], + [ sh:description "The relationship to the disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_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 30 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:order 43 ; + 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 48 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:p_value ], [ sh:class biolink:Publication ; sh:description "One or more 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 "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:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:timepoint ], + sh:path biolink:publications ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 5 ; - 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 26 ; - sh:path biolink:object_category_closure ], + sh:order 33 ; + 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 25 ; + sh:order 24 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Used to hold 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:Literal ; - sh:order 28 ; + sh:order 27 ; sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:iri ], + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ 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:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:boolean ; + 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 "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "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 3 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; + sh:order 11 ; sh:path biolink:knowledge_source ], - [ 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:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:phenotypic_state ] ; - sh:targetClass biolink:GeneToGeneCoexpressionAssociation . - -biolink:GeneToGeneFamilyAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - sh:closed true ; - sh:description "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." ; + sh: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 8 ; + sh:path biolink:qualifiers ] ; + 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:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Optional quantitative value indicating degree of expression." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + 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:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + 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:targetClass biolink:GeneExpressionMixin . + +biolink:GeneGroupingMixin a sh:NodeShape ; + sh:closed false ; + sh:description "any grouping of multiple genes or gene products" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ 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:GeneGroupingMixin . + +biolink:GeneHasVariantThatContributesToDiseaseAssociation 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 35 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; + sh:order 14 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "used to 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 24 ; + sh:path biolink:object_closure ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 4 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; + sh:order 29 ; sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "used to 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:nodeKind sh:Literal ; - sh:order 14 ; - 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:minCount 1 ; + sh:order 34 ; + sh:path biolink:id ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; + sh:minCount 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 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 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ 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 42 ; + sh:path biolink:has_count ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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 17 ; + sh:path biolink:timepoint ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 38 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "membership of the gene in the given gene family." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold 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:Literal ; - sh:order 35 ; - sh:path dct:description ], + sh:order 28 ; + 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 36 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; + sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_form_or_variant_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 22 ; + 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 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 43 ; + 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:nodeKind sh:Literal ; - sh:order 30 ; - 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: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 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 6 ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to 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:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ 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:order 20 ; + sh:path biolink:original_object ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 46 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 10 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:anyURI ; - 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 12 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], + sh:order 8 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - 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:description "used to 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 17 ; - sh:path biolink:subject_category ], + sh:order 18 ; + 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 5 ; + sh:order 9 ; sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 41 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], + sh:order 45 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; sh:description "Used to hold 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:Literal ; - sh:order 23 ; + sh:order 27 ; sh:path biolink:subject_namespace ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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_closure ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:order 44 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path dct:description ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:agent_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 31 ; + sh:path biolink:retrieval_source_ids ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; + sh:order 15 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 37 ; + sh:path rdf:type ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:boolean ; + 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:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 36 ; + sh:order 40 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ 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:datatype xsd:string ; + 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:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 48 ; + sh:path biolink:qualified_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; + sh:order 26 ; sh:path biolink:object_category_closure ], + [ 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:BlankNodeOrIRI ; + sh:order 1 ; + 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:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 21 ; - sh:path biolink:subject_category_closure ] ; - sh:targetClass biolink:GeneToGeneFamilyAssociation . + sh:path biolink:subject_category ] ; + sh:targetClass biolink:GeneHasVariantThatContributesToDiseaseAssociation . -biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:GeneToGeneAssociation ; +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:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:targetClass biolink:GeneProductIsoformMixin . + +biolink:GeneRegulatesGeneAssociation 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:description "Describes a regulatory relationship between two genes or gene products." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold 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 "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 35 ; + 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 26 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + 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:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; + sh:order 30 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - 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:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 40 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - 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 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: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:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 38 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; + sh:order 7 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_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 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - 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:description "Used to hold 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:order 27 ; + sh:path biolink:subject_namespace ], [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:Publication ; - sh:description "One or more 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:datatype xsd:anyURI ; - 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:Literal ; sh:order 15 ; - sh:path biolink:original_predicate ], + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "used to 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:Literal ; - sh:order 16 ; + sh:order 20 ; sh:path biolink:original_object ], - [ 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:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], [ 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:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 9 ; + sh:order 13 ; 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 10 ; + sh:path biolink:publications ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "homology relationship type" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject 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_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is 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: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:order 31 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + 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 9 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "used to 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:Literal ; - sh:order 14 ; + sh:order 18 ; sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "the aspect of the object gene or gene product that is being regulated, must be a descendant of \"activity_or_abundance\"\"" ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "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:Literal ; - sh:order 30 ; - sh:path biolink:id ], + sh:order 0 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ] ; - sh:targetClass biolink:GeneToGeneHomologyAssociation . - -biolink:GeneToGeneProductRelationship a sh:NodeShape ; - rdfs:subClassOf biolink:SequenceFeatureRelationship ; - sh:closed true ; - sh:description "A gene is transcribed and potentially translated to a gene product" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:GeneProductMixin ; + sh:order 37 ; + 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 21 ; + sh:path biolink:subject_category ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:agent_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 5 ; + sh:path rdf:predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 39 ; + 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 36 ; + sh:path biolink:category ], + [ sh:class biolink:GeneOrGeneProduct ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; + sh:order 6 ; sh:path rdf:object ], - [ sh:datatype xsd:anyURI ; - 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:nodeKind sh:Literal ; - sh:order 15 ; + sh:order 17 ; + sh:path biolink:timepoint ], + [ sh:class biolink:GeneOrGeneProduct ; + 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:BlankNodeOrIRI ; + sh:order 4 ; + 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 19 ; sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; + sh:order 8 ; sh:path biolink:qualifier ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:species_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 34 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object 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_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label 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_label_closure ] ; + sh:targetClass biolink:GeneRegulatesGeneAssociation . + +biolink:GeneToDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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:subject_label_closure ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; + sh:order 14 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 16 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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 22 ; - sh:path biolink:object_category_closure ], + sh:order 43 ; + 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 35 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - 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 12 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 32 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object label 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:object_label_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to 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 37 ; + 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 8 ; + sh:path biolink:qualifiers ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:sex_qualifier ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; + sh:order 9 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:object_category ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ 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:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 42 ; + 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 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 39 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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:nodeKind sh:Literal ; - sh:order 8 ; + sh:order 19 ; + 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 30 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:boolean ; + 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:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 36 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the 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:order 24 ; sh:path biolink:subject_category_closure ], - [ 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:datatype xsd:string ; + sh:description "An intermediate aggregator resource 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 "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 "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], + sh:order 20 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting 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 22 ; + 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 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:object_category_closure ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 44 ; + sh:path biolink:has_percentage ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:deprecated ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; + sh:order 15 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 41 ; + sh:path biolink:has_count ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], + sh:order 38 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 7 ; + sh:path biolink: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 48 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:order 47 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 31 ; + sh:path biolink:p_value ], + [ 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 "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:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "Used to hold 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:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the 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 27 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - 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:minCount 1 ; + sh:order 33 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "used to 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 17 ; - sh:path biolink:subject_category ] ; - sh:targetClass biolink:GeneToGeneProductRelationship . - -biolink:GeneToGoTermAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:FunctionalAssociation ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:path biolink: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:nodeKind sh:Literal ; - sh:order 15 ; + sh:order 18 ; sh:path biolink:original_predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - 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 namespace 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:Literal ; - 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 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Gene ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ 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:IRI ; + sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - 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 object 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_closure ] ; + sh:targetClass biolink:GeneToDiseaseAssociation . + +biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ 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:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "class describing the activity, process or localization of the gene product" ; + sh:order 4 ; + sh:path rdf:object ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:boolean ; + 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:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 14 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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 29 ; + 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:order 9 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "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:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 8 ; + 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 21 ; - sh:path biolink:subject_category_closure ], + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "used to 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:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 17 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + 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:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], - [ 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:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 47 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the phenotypic feature" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:subject ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; + sh:order 15 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 44 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; + sh:order 23 ; sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; + sh:order 13 ; sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "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:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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 "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 16 ; + 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 3 ; + sh:path rdf:predicate ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; + sh:order 31 ; sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - 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 18 ; + sh:order 21 ; sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ] ; - sh:targetClass biolink:GeneToGoTermAssociation . - -biolink:GeneToPathwayAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - 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:datatype xsd:anyURI ; - 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:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 9 ; + sh:order 12 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], - [ 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:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 48 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "A unique identifier 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:agent_type ], + sh:order 33 ; + 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 34 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject 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_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:Literal ; - sh:order 4 ; - sh:path biolink: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:order 5 ; + sh:path biolink:sex_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; + sh:order 20 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - 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:Literal ; - 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 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:class biolink:OntologyClass ; - sh:description "Used to hold the 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 "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; + sh:order 32 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "used to 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 "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 7 ; + sh:path biolink: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 35 ; + sh:path biolink:category ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 1 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:order 43 ; + sh:path biolink:has_quotient ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; + sh:order 11 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ 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:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; + sh:order 28 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - 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 25 ; + 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:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 36 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Used to hold 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:Literal ; - sh:order 23 ; + sh:order 26 ; 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 18 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "used to 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:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the gene or gene product entity that participates or influences the pathway" ; + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold 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: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 24 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:deprecated ], + [ 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:targetClass biolink:GeneToDiseaseOrPhenotypicFeatureAssociation . + +biolink:GeneToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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: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:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:IRI ; + sh:order 2 ; + 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:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:id ], + sh:order 1 ; + sh:path rdf:predicate ] ; + sh:targetClass biolink:GeneToEntityAssociationMixin . + +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:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which the gene is expressed" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path rdf:object ], + [ sh:description "expression relationship" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 3 ; + 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 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 17 ; + sh:path biolink:original_predicate ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; + sh:order 13 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 5 ; + sh:path biolink:negated ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ] ; - sh:targetClass biolink:GeneToPathwayAssociation . - -biolink:GeneToPhenotypicFeatureAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; sh:order 39 ; - sh:path biolink:has_attribute ], + sh:path biolink:deprecated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the 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:datatype xsd:string ; - sh:description "used to 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 "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - 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 10 ; - sh:path biolink:has_evidence ], + sh:order 6 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; + sh:order 28 ; sh:path biolink:object_label_closure ], - [ sh:datatype ; - 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:Literal ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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 5 ; - sh:path biolink:object_direction_qualifier ], + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; + sh:order 31 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], [ sh:datatype xsd:string ; - 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:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 47 ; - sh:path biolink:qualified_predicate ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 26 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:LifeStage ; + sh:description "stage at which the gene is expressed in the site" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:stage_qualifier ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; + sh:order 14 ; sh:path biolink:agent_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 9 ; - 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 33 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to 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:Literal ; - sh:order 7 ; - sh:path biolink: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 20 ; - sh:path biolink:subject_category ], + sh:order 16 ; + 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 34 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 22 ; + sh:order 21 ; 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 25 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 26 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:anyURI ; - 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 35 ; + sh:path rdf:type ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:object_closure ], + sh:order 30 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 12 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the phenotypic feature" ; + 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:BlankNodeOrIRI ; - sh:order 0 ; + sh:order 2 ; sh:path rdf:subject ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 37 ; + 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:OntologyClass ; + sh:description "can be used to indicate magnitude, or also ranking" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; + sh:nodeKind sh:IRI ; sh:order 1 ; - sh:path rdf:predicate ], + sh:path biolink:quantifier_qualifier ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_quotient ], - [ 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 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_count ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "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 object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:subject_aspect_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:order 18 ; + sh:path biolink:original_object ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], + sh:order 38 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an 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:nodeKind sh:Literal ; - sh:order 38 ; - sh:path dct:description ], + sh:order 25 ; + 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:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:p_value ], + sh:order 24 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 33 ; + sh:order 32 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - 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 9 ; + sh:path biolink:has_evidence ] ; + 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:datatype xsd:string ; + sh:description "Used to hold the 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 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:order 21 ; sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object 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:datatype xsd:string ; + sh:description "Used to hold the 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:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; + sh:order 3 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:knowledge_source ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_namespace ] ; - sh:targetClass biolink:GeneToPhenotypicFeatureAssociation . - -biolink:Genome a sh:NodeShape ; - rdfs:subClassOf biolink:BiologicalEntity ; - 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:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + 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:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 17 ; + 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 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], + sh:path biolink:has_evidence ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; + sh:order 37 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 1 ; + sh:order 30 ; sh:path biolink:id ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; + sh:description "used to 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:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:Genome . - -biolink:GenomicBackgroundExposure a sh:NodeShape ; - rdfs:subClassOf biolink:Attribute ; - 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:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + 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 5 ; + sh:path biolink:qualifiers ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 35 ; + sh:path dct:description ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - 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 12 ; + sh:path biolink:agent_type ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 36 ; + sh:path biolink:has_attribute ], + [ 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:Literal ; - sh:order 15 ; - sh:path biolink:category ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - 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 "used to 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:Literal ; - sh:order 6 ; - sh:path rdfs:label ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:has_biological_sequence ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:synonym ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 16 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 31 ; + 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 18 ; - sh:path biolink:has_attribute ], + sh:order 22 ; + sh:path biolink:object_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 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:full_name ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of 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_qualitative_value ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - 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 1 ; - sh:path biolink:has_gene_or_gene_product ], - [ sh:datatype xsd:time ; - 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:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 8 ; - sh:path biolink:has_quantitative_value ] ; - sh:targetClass biolink:GenomicBackgroundExposure . - -biolink:GenomicEntity a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; + 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:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ] ; - sh:targetClass biolink:GenomicEntity . + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource 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:GeneToGeneAssociation . -biolink:GenomicSequenceLocalization a sh:NodeShape ; - rdfs:subClassOf biolink:SequenceAssociation ; +biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; sh:closed true ; - sh:description "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." ; + sh:description "Indicates that two genes are co-expressed, generally under the same conditions." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 28 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:property [ sh:class biolink:LifeStage ; + sh:description "stage during which gene or protein expression of takes place." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 35 ; - sh:path biolink:id ], - [ 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: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:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 6 ; sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 34 ; + sh:path biolink:id ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; + sh:order 39 ; sh:path dct:description ], - [ 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:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:category ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; + sh:order 32 ; sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 14 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 36 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:integer ; - 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:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:end_interbase_coordinate ], + sh:order 41 ; + sh:path biolink:deprecated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of 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: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 11 ; + sh:order 10 ; sh:path biolink:publications ], - [ sh:datatype xsd:integer ; - 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:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:start_interbase_coordinate ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 20 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdf:type ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; + sh:order 17 ; 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 27 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], - [ 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 10 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 29 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_closure ], + sh:order 21 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 22 ; - sh:path biolink:subject_category ], - [ sh:description "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2." ; - sh:in ( "0" "1" "2" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:phase ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:path biolink:object_category ], + [ 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:order 16 ; - sh:path biolink:knowledge_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:nodeKind sh:BlankNodeOrIRI ; + sh:order 4 ; + sh:path rdf:subject ], + [ sh:datatype xsd:boolean ; + 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:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 23 ; - 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 32 ; - sh:path biolink:retrieval_source_ids ], - [ 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:order 40 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:iri ], + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object 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: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 26 ; + sh:order 25 ; 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 26 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], + [ 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 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:Literal ; - sh:order 6 ; + sh:order 5 ; sh:path rdf:predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 19 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:qualifier ], + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:agent_type ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_evidence ] ; - sh:targetClass biolink:GenomicSequenceLocalization . - -biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:GenotypeToDiseaseAssociation ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:Genotype ; - sh:description "A genotype that has a role in modeling the disease." ; + sh:order 11 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 37 ; + sh:path rdf:type ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; 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 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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 6 ; - sh:path biolink:publications ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:subject_direction_qualifier ], + sh:order 15 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; + sh:order 33 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold 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:Literal ; - sh:order 23 ; + sh:order 27 ; sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - 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 29 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 28 ; + 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:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], + sh:order 19 ; + 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 35 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "The relationship to the disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - 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 23 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path biolink:qualifier ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 5 ; + sh:order 9 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - 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:class biolink:OntologyClass ; + sh:description "Optional quantitative value indicating degree of expression." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:quantifier_qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to 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 41 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "used to 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 18 ; - 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:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:anyURI ; - 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:knowledge_source ], + [ 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:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 1 ; + sh:path biolink:expression_site ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 38 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:GeneToGeneCoexpressionAssociation . + +biolink:GeneToGeneFamilyAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the 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 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 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 32 ; + sh:path biolink:category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - 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:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 24 ; - 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 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype ; - 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:Literal ; - sh:order 43 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 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 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "used to 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:Literal ; sh:order 14 ; sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold 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:Literal ; - sh:order 34 ; - sh:path rdfs:label ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:subject_aspect_qualifier ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource 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:datatype xsd:string ; + sh:description "Used to hold the 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:datatype xsd:string ; + sh:description "Used to hold the object 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:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "used to 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:Literal ; sh:order 16 ; sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; @@ -14191,793 +13225,476 @@ biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of 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:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 35 ; 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 21 ; - sh:path biolink:subject_category_closure ] ; - sh:targetClass biolink:GenotypeAsAModelOfDiseaseAssociation . - -biolink:GenotypeToEntityAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ 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:description "Used to hold the 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:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "membership of the gene in the given gene family." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:Genotype ; - sh:description "genotype that is the subject of the association" ; + [ 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:targetClass biolink:GenotypeToEntityAssociationMixin . - -biolink:GenotypeToGeneAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - 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:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:id ], + sh:order 34 ; + 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:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; sh:order 33 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "used to 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: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:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Genotype ; - sh:description "parent genotype" ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Gene ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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 11 ; - sh:path biolink:knowledge_level ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 18 ; + sh:path biolink:object_category ] ; + 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:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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 12 ; - sh:path biolink:agent_type ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of 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 "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:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - 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:datatype xsd:string ; - sh:description "the relationship type used to connect genotype to gene" ; + sh:order 17 ; + 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 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Gene ; - sh:description "gene implicated in genotype" ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:anyURI ; - 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 11 ; + sh:path biolink:knowledge_level ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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 unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 9 ; - 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: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:datatype xsd:string ; - sh:description "used to 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 "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - 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:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "used to 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:Literal ; - sh:order 3 ; - sh:path biolink:negated ] ; - sh:targetClass biolink:GenotypeToGeneAssociation . - -biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - sh:closed true ; - sh:description "Any association between one genotype and a genotypic entity that is a sub-component of it" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:RetrievalSource ; + sh:order 16 ; + 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 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:class biolink: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:Literal ; - sh:order 30 ; - sh:path biolink:id ], + sh:nodeKind sh:BlankNodeOrIRI ; + 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 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:description "Used to hold the 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 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 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "used to 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:Literal ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ 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:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:deprecated ], - [ sh:class biolink:Genotype ; - sh:description "child 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 22 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; sh:order 33 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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 35 ; + sh:path dct:description ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + 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 32 ; + sh:path biolink:category ], + [ 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:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "homology relationship type" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; 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:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 31 ; - 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 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ] ; + sh:targetClass biolink:GeneToGeneHomologyAssociation . + +biolink:GeneToGeneProductRelationship a sh:NodeShape ; + sh:closed true ; + sh:description "A gene is transcribed and potentially translated to a gene product" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink: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:class biolink:Genotype ; - sh:description "parent genotype" ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - 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 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 35 ; sh:path dct:description ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is 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:targetClass biolink:GenotypeToGenotypePartAssociation . - -biolink:GenotypeToPhenotypicFeatureAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - 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:datatype xsd:anyURI ; - 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:object_category ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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 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:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ], + sh:order 37 ; + sh:path biolink:deprecated ], + [ 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:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 28 ; + sh:path biolink:p_value ], + [ 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 46 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:double ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_quotient ], - [ sh:class biolink:Publication ; - sh:description "One or more 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:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_percentage ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:boolean ; - 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:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:class biolink:Genotype ; - sh:description "genotype that is associated with the phenotypic feature" ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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 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:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; + 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 28 ; - 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 32 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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 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:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:order 16 ; + 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 23 ; + sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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:datatype xsd:string ; + sh:description "An intermediate aggregator resource 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:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype ; - 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:Literal ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "A unique 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:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 10 ; - 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 30 ; + 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 19 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], + 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 18 ; + sh:order 17 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular 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:Literal ; - sh:order 39 ; - sh:path biolink:has_count ], - [ sh:class biolink:PhenotypicFeature ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], + [ 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 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - 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 6 ; - 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 8 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "Used to hold 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 44 ; - sh:path biolink:subject_direction_qualifier ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; + sh:order 4 ; sh:path biolink:qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:class biolink:Gene ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 31 ; - sh:path biolink:id ], + 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: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:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ] ; - sh:targetClass biolink:GenotypeToPhenotypicFeatureAssociation . + sh:order 5 ; + sh:path biolink:qualifiers ] ; + sh:targetClass biolink:GeneToGeneProductRelationship . -biolink:GenotypeToVariantAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; +biolink:GeneToGoTermAssociation 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:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; @@ -14986,56 +13703,121 @@ biolink:GenotypeToVariantAssociation a sh:NodeShape ; sh:order 18 ; sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:boolean ; + 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:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ 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:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the 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:RetrievalSource ; - sh:description "A list of 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 "class describing the activity, process or localization of the gene product" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:anyURI ; - 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 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:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 31 ; - sh:path biolink:iri ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "used to 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:Literal ; sh:order 16 ; sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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 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 subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + 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 6 ; + sh:path biolink:publications ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -15043,4781 +13825,1015 @@ biolink:GenotypeToVariantAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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: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:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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: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:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is 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:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold 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:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; sh:order 30 ; - sh:path biolink:id ], - [ 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:path biolink:id ] ; + 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 "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:datatype xsd:string ; - sh:description "the relationship type used to connect genotype to gene" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 9 ; + 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 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of 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:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "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 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 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; sh:order 33 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], + sh:order 35 ; + 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 6 ; sh:path biolink:publications ], + [ 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:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource 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:datatype xsd:string ; sh:description "Used to hold 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:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], - [ 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:datatype xsd:time ; - sh:description "a point in time" ; + sh:description "Used to hold the subject 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:datatype xsd:string ; + sh:description "Used to hold 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:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + 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:description "Used to hold the 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:class biolink:Genotype ; - sh:description "parent genotype" ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "used to 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:GeneOrGeneProduct ; + sh:description "the gene or gene product entity that participates or influences the pathway" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:BlankNodeOrIRI ; 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 7 ; - sh:path biolink:has_evidence ] ; - sh:targetClass biolink:GenotypeToVariantAssociation . - -biolink:GenotypicSex a sh:NodeShape ; - rdfs:subClassOf biolink:BiologicalSex ; - sh:closed true ; - sh:description "An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ 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 biolink:has_attribute_type ], + sh:order 34 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - 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:datatype xsd:string ; - 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 "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 5 ; + sh:order 30 ; sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 7 ; + 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:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + sh:description "used to 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:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; + sh:order 37 ; sh:path biolink:deprecated ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - 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:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; + sh:order 31 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ] ; - sh:targetClass biolink:GenotypicSex . - -biolink:GeographicExposure a sh:NodeShape ; - rdfs:subClassOf biolink:EnvironmentalExposure ; - 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:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; sh:order 11 ; - sh:path biolink:category ], - [ 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:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 14 ; + sh:order 36 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], - [ 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:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdfs:label ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:GeographicExposure . + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the 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:targetClass biolink:GeneToPathwayAssociation . -biolink:GeographicLocationAtTime a sh:NodeShape ; - rdfs:subClassOf biolink:GeographicLocation ; +biolink:GeneToPhenotypicFeatureAssociation 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:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:property [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the phenotypic feature" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:path rdf:subject ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ], + sh:order 16 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "used to 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:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 41 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:object_category_closure ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 38 ; sh:path dct:description ], - [ 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 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "latitude" ; + sh:order 20 ; + 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 24 ; + sh:path biolink:subject_category_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:latitude ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 37 ; + sh:path rdfs:label ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "longitude" ; + sh:order 44 ; + 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:Literal ; - sh:order 2 ; - sh:path biolink:longitude ], - [ sh:datatype xsd:string ; - 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 3 ; + sh:path biolink:sex_qualifier ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ] ; - sh:targetClass biolink:GeographicLocationAtTime . - -biolink:GrossAnatomicalStructure a sh:NodeShape ; - rdfs:subClassOf biolink:AnatomicalEntity ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 14 ; + sh:path biolink:knowledge_level ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; + sh:order 15 ; + sh:path biolink:agent_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 9 ; + sh:path biolink:publications ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 35 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:description "An intermediate aggregator resource 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:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:description "Used to hold the object 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_closure ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the 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:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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:order 42 ; + 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 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 30 ; + 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 21 ; + 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 10 ; + 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 18 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:boolean ; + 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:Attribute ; - sh:description "may often be an organism attribute" ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 39 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ 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:Literal ; - sh:order 6 ; - sh:path biolink:id ] ; - sh:targetClass biolink:GrossAnatomicalStructure . - -biolink:Haplotype a sh:NodeShape ; - rdfs:subClassOf biolink:BiologicalEntity ; - 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:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 9 ; - sh:path biolink:category ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:iri ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; sh:order 11 ; - sh:path rdfs:label ], + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; + sh:description "Used to hold 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:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 27 ; + 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:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:id ], + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label 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:object_label_closure ], + [ sh:datatype xsd:string ; + 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 47 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 36 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; + sh:order 40 ; sh:path biolink:deprecated ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "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 4 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:object_direction_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 48 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to 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 19 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:datatype xsd:string ; + sh:description "Used to hold the subject 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:subject_label_closure ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:order 43 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - 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:minCount 1 ; + sh:order 33 ; + sh:path biolink:id ] ; + 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 "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ 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:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + 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:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:iri ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + 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 2 ; 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:datatype xsd:string ; - 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 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:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:full_name ] ; - sh:targetClass biolink:Haplotype . + 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 9 ; + sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ] ; + sh:targetClass biolink:Genome . -biolink:Hospitalization a sh:NodeShape ; - rdfs:subClassOf biolink:ClinicalIntervention ; +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:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 4 ; + sh:path biolink:in_taxon_label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 10 ; + 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:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 6 ; + sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:order 17 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 16 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 10 ; + sh:order 18 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 6 ; - sh:path biolink:category ], + [ sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:has_biological_sequence ], + [ 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:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 4 ; + sh:order 5 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:Hospitalization . - -biolink:HospitalizationOutcome a sh:NodeShape ; - sh:closed true ; - sh:description "An outcome resulting from an exposure event which is the increased manifestation of acute (e.g. emergency room visit) or chronic (inpatient) hospitalization." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:HospitalizationOutcome . - -biolink:Human a sh:NodeShape ; - rdfs:subClassOf biolink:Mammal ; - sh:closed true ; - sh:description "A member of the the species Homo sapiens." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - 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:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:Human . - -biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - 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:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of 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:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ 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:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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 36 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - 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:Literal ; - 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 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is 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:datatype xsd:anyURI ; - 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:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - 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:class biolink:OntologyClass ; - sh:description "Used to hold the 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:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 16 ; - sh:path biolink:original_object ] ; - sh:targetClass biolink:InformationContentEntityToNamedThingAssociation . - -biolink:Invertebrate a sh:NodeShape ; - rdfs:subClassOf biolink:CellularOrganism ; - 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:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ] ; - sh:targetClass biolink:Invertebrate . - -biolink:JournalArticle a sh:NodeShape ; - rdfs:subClassOf biolink:Article ; - 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:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:keywords ], - [ sh:datatype xsd:string ; - sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:issue ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:iso_abbreviation ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:format ], - [ sh:datatype xsd:anyURI ; - sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:published_in ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - 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:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 20 ; - sh:path biolink:category ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path dct:type ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:pages ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:volume ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:mesh_terms ], - [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:summary ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 22 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:id ] ; - sh:targetClass biolink:JournalArticle . - -biolink:LogOddsAnalysisResult a sh:NodeShape ; - rdfs:subClassOf biolink:StudyResult ; - sh:closed true ; - sh:description "A result of a log odds ratio analysis." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 8 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ] ; - sh:targetClass biolink:LogOddsAnalysisResult . - -biolink:MacromolecularComplex a sh:NodeShape ; - rdfs:subClassOf biolink:BiologicalEntity ; - sh:closed true ; - sh:description "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 7 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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 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:targetClass biolink:MacromolecularComplex . - -biolink:MacromolecularMachineToBiologicalProcessAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:FunctionalAssociation ; - 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 "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:class biolink:BiologicalProcess ; - sh:description "class describing the activity, process or localization of the gene product" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - 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 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:Publication ; - sh:description "One or more 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:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - 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:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - 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 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - 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 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ 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:BlankNodeOrIRI ; - 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 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - 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 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:MacromolecularMachineToBiologicalProcessAssociation . - -biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:FunctionalAssociation ; - 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:class biolink:OntologyClass ; - sh:description "Used to hold the 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:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - 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:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_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:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:CellularComponent ; - sh:description "class describing the activity, process or localization of the gene product" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], - [ 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:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - 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:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - 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:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the 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:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ] ; - sh:targetClass biolink:MacromolecularMachineToCellularComponentAssociation . - -biolink:MacromolecularMachineToEntityAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:description "an association which has a macromolecular machine mixin as a subject" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - 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:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; - sh:targetClass biolink:MacromolecularMachineToEntityAssociationMixin . - -biolink:MacromolecularMachineToMolecularActivityAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:FunctionalAssociation ; - sh:closed true ; - sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink: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:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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 36 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink: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:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ 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:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - 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:Literal ; - 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 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is 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:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is 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:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - 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:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ] ; - sh:targetClass biolink:MacromolecularMachineToMolecularActivityAssociation . - -biolink:MappingCollection a sh:NodeShape ; - sh:closed false ; - sh:description "A collection of deprecated mappings." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:PredicateMapping ; - sh:description "A collection of relationships that are not used in biolink, but have biolink patterns that can be used to replace them. This is a temporary slot to help with the transition to the fully qualified predicate model in Biolink3." ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path biolink:predicate_mappings ] ; - sh:targetClass biolink:MappingCollection . - -biolink:MaterialSampleDerivationAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - 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:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - 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 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "derivation relationship" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - 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 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:MaterialSample ; - sh:description "the material sample being described" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the 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 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - 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: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:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - 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 36 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ] ; - sh:targetClass biolink:MaterialSampleDerivationAssociation . - -biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - sh:closed true ; - sh:description "An association between a material sample and a disease or phenotype." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 30 ; - 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 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is 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:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ 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:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - 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:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ 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:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - 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 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - 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 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - 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 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - 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:Literal ; - 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 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ 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:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . - -biolink:MaterialSampleToEntityAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:description "An association between a material sample and something." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ 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:datatype xsd:string ; - 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:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ] ; - sh:targetClass biolink:MaterialSampleToEntityAssociationMixin . - -biolink:MicroRNA a sh:NodeShape ; - rdfs:subClassOf biolink:NoncodingRNAProduct ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - 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: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:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:MicroRNA . - -biolink:ModelToDiseaseAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:description "This mixin is used for any association class for which the subject (source node) plays the role of a 'model', in that it recapitulates some features of the disease in a way that is useful for studying the disease outside a patient carrying the disease" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "The relationship to the disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "The entity that serves as the model of the disease. This may be an organism, a strain of organism, a genotype or variant that exhibits similar features, or a gene that when mutated exhibits features of the disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; - sh:targetClass biolink:ModelToDiseaseAssociationMixin . - -biolink:MolecularActivityToChemicalEntityAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - 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:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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 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:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - 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:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - 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:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 30 ; - 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:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh: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:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ] ; - sh:targetClass biolink:MolecularActivityToChemicalEntityAssociation . - -biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - 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:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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 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 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:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - 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:Literal ; - 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 36 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], - [ 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 "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:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink: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:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - 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 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the 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:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ 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:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ] ; - sh:targetClass biolink:MolecularActivityToMolecularActivityAssociation . - -biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - 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: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:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Pathway ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is 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:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_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 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], - [ 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:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - 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:datatype xsd:string ; - 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:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - 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 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - 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 22 ; - 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 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ] ; - sh:targetClass biolink:MolecularActivityToPathwayAssociation . - -biolink:MortalityOutcome a sh:NodeShape ; - sh:closed true ; - sh:description "An outcome of death from resulting from an exposure event." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:MortalityOutcome . - -biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - sh:closed true ; - sh:description "" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 35 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:object_context_qualifier ], - [ sh:datatype xsd:string ; - 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:Literal ; - sh:order 3 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdf:type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 19 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:subject_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - 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 11 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 14 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 21 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - 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 26 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 20 ; - sh:path biolink:original_predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - 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 27 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh: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 12 ; - 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 23 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], - [ 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 7 ; - sh:path biolink:population_context_qualifier ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - 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 32 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 29 ; - 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 10 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path dct:description ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 28 ; - sh:path biolink:subject_namespace ] ; - sh:targetClass biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . - -biolink:NucleicAcidSequenceMotif a sh:NodeShape ; - rdfs:subClassOf biolink:BiologicalEntity ; - 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:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - 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:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; - sh:path biolink:category ] ; - sh:targetClass biolink:NucleicAcidSequenceMotif . - -biolink:NucleosomeModification a sh:NodeShape ; - rdfs:subClassOf biolink:BiologicalEntity ; - 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:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - 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:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 7 ; - sh:path biolink:id ] ; - sh:targetClass biolink:NucleosomeModification . - -biolink:ObservedExpectedFrequencyAnalysisResult a sh:NodeShape ; - rdfs:subClassOf biolink:StudyResult ; - sh:closed true ; - sh:description "A result of a observed expected frequency analysis." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 8 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ] ; - sh:targetClass biolink:ObservedExpectedFrequencyAnalysisResult . - -biolink:OrganismTaxonToEntityAssociation a sh:NodeShape ; - sh:closed false ; - sh:description "An association between an organism taxon and another entity" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "organism 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:datatype xsd:string ; - 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:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ] ; - sh:targetClass biolink:OrganismTaxonToEntityAssociation . - -biolink:OrganismTaxonToEnvironmentAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - 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:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ 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:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 30 ; - 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 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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 22 ; - sh:path biolink:object_category_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:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - 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 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ 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:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - 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 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "predicate describing the relationship between the taxon and the environment" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ] ; - sh:targetClass biolink:OrganismTaxonToEnvironmentAssociation . - -biolink:OrganismTaxonToOrganismTaxonInteraction a sh:NodeShape ; - rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonAssociation ; - sh:closed true ; - sh:description "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the taxon that is the subject of the association" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the taxon that is the subject of the association" ; + sh:order 7 ; + sh:path biolink:has_attribute_type ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 14 ; + sh:path biolink:synonym ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 8 ; + sh:path biolink:has_quantitative_value ], + [ 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 rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 3 ; + sh:path biolink:in_taxon ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - 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 23 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], + sh:order 9 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; + sh:order 19 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - 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 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "the environment in which the two taxa interact" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:associated_environmental_context ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:aggregator_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - 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 8 ; - sh:path biolink:has_evidence ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:path biolink:provided_by ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 10 ; - 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: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:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; + 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 12 ; + 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:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - 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 19 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 15 ; + sh:path biolink:category ] ; + sh:targetClass biolink:GenomicBackgroundExposure . + +biolink:GenomicEntity a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ] ; - sh:targetClass biolink:OrganismTaxonToOrganismTaxonInteraction . + sh:order 0 ; + sh:path biolink:has_biological_sequence ] ; + sh:targetClass biolink:GenomicEntity . -biolink:OrganismTaxonToOrganismTaxonSpecialization a sh:NodeShape ; - rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonAssociation ; +biolink:GenomicSequenceLocalization a sh:NodeShape ; sh:closed true ; - sh:description "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" ; + sh:description "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Publication ; - sh:description "One or more 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:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - 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 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ 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:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:order 9 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; + sh:order 38 ; sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the more general taxon" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:anyURI ; - 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 40 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object 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 "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:Literal ; - sh:order 15 ; + sh:order 20 ; sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], + sh:order 14 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:adjusted_p_value ], + [ 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:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], + sh:order 23 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the 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 "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:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:path biolink:phase ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; + sh:order 17 ; sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - 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 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "used to 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 biolink:object_namespace ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 42 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the 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:order 26 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the more specific taxon" ; - 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 0 ; - sh:path rdf:subject ], + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], + [ 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:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 19 ; + sh:path biolink:original_subject ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; + sh:order 13 ; sh:path biolink:knowledge_source ], - [ 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:datatype xsd:boolean ; + 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 "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 15 ; + sh:path biolink:aggregator_knowledge_source ], + [ 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:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 5 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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:datatype xsd:string ; + sh:description "used to 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:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; + sh:order 16 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:boolean ; - 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:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 18 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 30 ; + sh:order 35 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:integer ; + 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:nodeKind sh:Literal ; - sh:order 35 ; - 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:order 1 ; + sh:path biolink:end_interbase_coordinate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the 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:retrieval_source_ids ] ; - sh:targetClass biolink:OrganismTaxonToOrganismTaxonSpecialization . - -biolink:OrganismToOrganismAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:path biolink: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 37 ; + sh:path biolink:category ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 36 ; + 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 22 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:integer ; + 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:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "Used to hold 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:Literal ; - sh:order 23 ; + sh:order 28 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 41 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:GenomicSequenceLocalization . + +biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the 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: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:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - 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:Literal ; - 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 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 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:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is 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:publications ], + sh:order 18 ; + sh:path biolink:object_category ], + [ 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:datatype xsd:string ; - sh:description "used to 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 "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 38 ; + sh:path biolink:subject_aspect_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:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; sh:order 30 ; sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold 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:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 24 ; + 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 "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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:datatype xsd:string ; + 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:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:order 42 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:Publication ; + sh:description "One or more 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:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 40 ; + sh:path biolink:object_aspect_qualifier ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -19825,1105 +14841,1282 @@ biolink:OrganismToOrganismAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 43 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:object_direction_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 32 ; + sh:path biolink:category ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "used to 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:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of 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:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; sh:order 33 ; 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:datatype xsd:string ; + sh:description "Used to hold the 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:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - 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:order 36 ; + 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 27 ; - sh:path biolink:retrieval_source_ids ], - [ 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:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "The relationship to the disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Genotype ; + sh:description "A genotype that has a role in modeling the disease." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is 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:IndividualOrganism ; - sh:description "An association between two individual organisms." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the 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 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold 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:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:path biolink:object_label_closure ] ; + sh:targetClass biolink:GenotypeAsAModelOfDiseaseAssociation . + +biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold 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:Publication ; + sh:description "One or more 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:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], + 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:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is 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:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - 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:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - 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 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - 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 5 ; - sh:path biolink:qualifiers ] ; - sh:targetClass biolink:OrganismToOrganismAssociation . - -biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:anyURI ; - 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 "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + 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 32 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - 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 "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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 unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - 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:datatype xsd:boolean ; + 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 "E.g. is pathogenic for" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 39 ; sh:path biolink:subject_direction_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 15 ; + 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 31 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 38 ; + 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 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:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the 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 22 ; - sh:path biolink:object_category_closure ], + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:class biolink:Genotype ; + sh:description "a genotype that is associated in some way with a disease state" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - 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: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:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:qualified_predicate ], + sh:order 43 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:class biolink:Disease ; - sh:description "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:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + 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:nodeKind sh:Literal ; - sh:order 31 ; - 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 42 ; + sh:path biolink:qualified_predicate ] ; + sh:targetClass biolink:GenotypeToDiseaseAssociation . + +biolink:GenotypeToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Genotype ; + sh:description "genotype that is the subject of the association" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ 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:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ] ; + sh:targetClass biolink:GenotypeToEntityAssociationMixin . + +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:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; sh:order 33 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - 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 "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:object_direction_qualifier ], + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - 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 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:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ 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:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 35 ; sh:path dct:description ], - [ 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:RetrievalSource ; + sh:description "A list of 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 relationship type used to connect genotype to gene" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:class biolink:OntologyClass ; + sh:description "Used to hold the 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:datatype xsd:string ; - sh:description "used to 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: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:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to 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:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "The relationship to the disease" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + 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:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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:datatype xsd:string ; + sh:description "A unique identifier 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:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Genotype ; + sh:description "parent genotype" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + 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 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:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:frequency_qualifier ], + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "used to 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:datatype xsd:string ; + sh:description "Used to hold the 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:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 12 ; + sh:path biolink:agent_type ], + [ 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:Gene ; + sh:description "gene implicated in genotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "used to 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 "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An intermediate aggregator resource 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 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold 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:Literal ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ] ; - sh:targetClass biolink:OrganismalEntityAsAModelOfDiseaseAssociation . + 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:targetClass biolink:GenotypeToGeneAssociation . -biolink:PairwiseMolecularInteraction a sh:NodeShape ; - rdfs:subClassOf biolink:PairwiseGeneToGeneInteraction ; +biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; sh:closed true ; - sh:description "An interaction at the molecular level between two physical entities" ; + 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:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "An intermediate aggregator resource 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:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + 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 7 ; + sh:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Genotype ; + sh:description "child genotype" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 13 ; + 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:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "identifier for the interaction. This may come from an interaction database such as IMEX." ; + sh:description "Used to hold the 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:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_object ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to 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:nodeKind sh:Literal ; - sh:order 15 ; - 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 8 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], + sh:minCount 1 ; + sh:order 30 ; + 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 31 ; + 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 22 ; + sh:order 21 ; sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold 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:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; + sh:order 3 ; sh:path biolink:negated ], - [ sh:datatype xsd:string ; - 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 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 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; + sh:order 34 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "interaction relationship type" ; + [ sh:class biolink:Genotype ; + sh:description "parent genotype" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:interacting_molecules_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ 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:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; + sh:order 29 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold 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:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the 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 ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ 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:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - 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 28 ; - sh:path biolink:retrieval_source_ids ], + sh:order 15 ; + 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:description "Used to hold the biolink class/category of an association. This is 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:qualifiers ], + sh:order 18 ; + 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 19 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 17 ; + 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 32 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "used to 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:Literal ; sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:path biolink:original_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:datatype xsd:string ; + sh:description "Used to hold the object 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:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ] ; - sh:targetClass biolink:PairwiseMolecularInteraction . + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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:targetClass biolink:GenotypeToGenotypePartAssociation . -biolink:Patent a sh:NodeShape ; - rdfs:subClassOf biolink:Publication ; +biolink:GenotypeToPhenotypicFeatureAssociation 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: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:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + 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 7 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + sh:description "Used to hold 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:Literal ; - sh:order 2 ; - sh:path biolink:summary ], + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; + sh:description "Used to hold the 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:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:rights ], + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:has_total ], [ sh:datatype xsd:string ; - 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 "Used to hold 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:Literal ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:order 24 ; + sh:path biolink:subject_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 2 ; + sh:path rdf:object ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource 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:datatype xsd:string ; + sh:description "used to 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:class biolink:RetrievalSource ; + sh:description "A list of 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:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:creation_date ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the 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 "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; + sh:order 37 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], + sh:description "Used to hold the 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:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:license ], + sh:order 43 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:format ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:mesh_terms ], - [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:keywords ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:path biolink:knowledge_source ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - 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 0 ; - sh:path biolink:authors ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:pages ], - [ sh:datatype xsd:string ; - 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 48 ; + sh:path biolink:frequency_qualifier ], + [ 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:Literal ; - sh:order 14 ; - sh:path biolink:id ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; + sh:order 38 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 44 ; + sh:path biolink:subject_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 6 ; - sh:path dct:type ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + 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:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:category ] ; - sh:targetClass biolink:Patent . - -biolink:PathognomonicityQuantifier a sh:NodeShape ; - rdfs:subClassOf biolink:SpecificityQuantifier ; - sh:closed false ; - sh:description "A relationship quantifier between a variant or symptom and a disease, which is high when the presence of the feature implies the existence of the disease" ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:PathognomonicityQuantifier . - -biolink:PathologicalAnatomicalExposure a sh:NodeShape ; - rdfs:subClassOf biolink:Attribute ; - 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:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:object_direction_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 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Genotype ; + sh:description "genotype that is associated with the phenotypic feature" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:order 39 ; + sh:path biolink:has_count ], [ sh:datatype xsd:string ; - 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 "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:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdfs:label ], + sh:order 47 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; + sh:description "Used to hold the subject 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:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; sh:order 8 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object 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 "connects an attribute to a class that describes it" ; + sh:description "Used to hold the biolink class/category 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 biolink:has_attribute_type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; sh:order 3 ; - sh:path biolink:has_quantitative_value ], + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:time ; - 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:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:order 45 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "used to 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:Literal ; - sh:order 9 ; - sh:path biolink:full_name ] ; - sh:targetClass biolink:PathologicalAnatomicalExposure . - -biolink:PathologicalAnatomicalOutcome a sh:NodeShape ; - sh:closed true ; - sh:description "An outcome resulting from an exposure event which is the manifestation of an abnormal anatomical structure." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:PathologicalAnatomicalOutcome . + 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:targetClass biolink:GenotypeToPhenotypicFeatureAssociation . -biolink:PathologicalAnatomicalStructure a sh:NodeShape ; - rdfs:subClassOf biolink:AnatomicalEntity ; +biolink:GenotypeToVariantAssociation 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:description "Any association between a genotype and a sequence variant." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is 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:in_taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 6 ; + sh:order 30 ; sh:path biolink:id ], [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 36 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 11 ; + 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 32 ; + sh:path biolink:category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the 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:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:description "Used to hold the 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:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold 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:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - 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 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ 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:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "used to 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:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:PathologicalAnatomicalStructure . - -biolink:PathologicalEntityMixin a sh:NodeShape ; - sh:closed false ; - sh:description "A pathological (abnormal) structure or process." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:PathologicalEntityMixin . - -biolink:PathologicalProcess a sh:NodeShape ; - rdfs:subClassOf biolink:BiologicalProcess ; - 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:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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:Genotype ; + sh:description "parent genotype" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 "Used to hold the 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 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path biolink:category ], + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - 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:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "Used to hold 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:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - 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 "Used to hold the object 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:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 10 ; - 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:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:SequenceVariant ; + sh:description "gene implicated in genotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path biolink:has_output ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:path rdf:object ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + 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 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Publication ; + sh:description "One or more 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 relationship type used to connect genotype to gene" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:order 1 ; - sh:path biolink:has_input ] ; - sh:targetClass biolink:PathologicalProcess . + 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:targetClass biolink:GenotypeToVariantAssociation . -biolink:PathologicalProcessExposure a sh:NodeShape ; - rdfs:subClassOf biolink:Attribute ; +biolink:GenotypicSex 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:description "An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 6 ; + sh:order 5 ; sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; + sh:path biolink:deprecated ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:synonym ], + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + 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 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], + 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 4 ; + sh:order 3 ; sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 13 ; + sh:path biolink:has_attribute ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; sh:path dct:description ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ 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:Literal ; sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - 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:Literal ; - sh:order 1 ; 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 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:targetClass biolink:GenotypicSex . + +biolink:GeographicExposure a sh:NodeShape ; + sh:closed true ; + sh:description "A geographic exposure is a factor relating to geographic proximity to some impactful entity." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:deprecated ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], + 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 ; @@ -20931,1594 +16124,1310 @@ biolink:PathologicalProcessExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:string ; + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:description "a human-readable description of an entity" ; + 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 11 ; + sh:path biolink:category ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 3 ; - sh:path biolink:has_quantitative_value ] ; - sh:targetClass biolink:PathologicalProcessExposure . - -biolink:PathologicalProcessOutcome a sh:NodeShape ; - sh:closed true ; - sh:description "An outcome resulting from an exposure event which is the manifestation of a pathological process." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:PathologicalProcessOutcome . + 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 "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 8 ; + sh:path biolink:xref ] ; + sh:targetClass biolink:GeographicExposure . -biolink:Phenomenon a sh:NodeShape ; - rdfs:subClassOf biolink:NamedThing ; +biolink:GeographicLocation 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:description "a location that can be described in lat/long coordinates" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:datatype xsd:float ; + sh:description "latitude" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; + sh:order 0 ; + sh:path biolink:latitude ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; + sh:description "A unique identifier 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:datatype xsd:float ; + sh:description "longitude" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:longitude ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; + sh:order 2 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], + 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 10 ; + sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 6 ; + sh:order 8 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path dct:description ] ; - sh:targetClass biolink:Phenomenon . + 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 long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ] ; + sh:targetClass biolink:GeographicLocation . -biolink:PhenotypicFeatureToDiseaseAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; +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:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:property [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; + 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 8 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:knowledge_source ], + sh:path biolink:category ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 6 ; + sh:path biolink:synonym ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "latitude" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 1 ; + sh:path biolink:latitude ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - 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:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + 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 4 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:float ; + sh:description "longitude" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 2 ; + sh:path biolink:longitude ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - 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 22 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 7 ; + sh:path biolink:id ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:has_count ], + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to 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:type ] ; + sh:targetClass biolink:GeographicLocationAtTime . + +biolink:GrossAnatomicalStructure 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:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh: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 biolink:in_taxon_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:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ 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 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:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:sex_qualifier ], + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], + 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:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; + sh:order 13 ; sh:path biolink:deprecated ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ] ; + 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: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:datatype xsd:string ; - sh:description "Used to hold 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 value in this node property represents the knowledge provider that created or assembled the node 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:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 12 ; + sh:path dct:description ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:class biolink:PhenotypicFeature ; - 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 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ 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 rdf:subject ], - [ sh:datatype xsd:double ; + 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:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 31 ; + sh:order 1 ; sh:path biolink:id ], - [ sh:class biolink:Disease ; - sh:description "disease" ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + 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 "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 3 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_percentage ], + sh:order 0 ; + sh:path biolink:has_biological_sequence ] ; + sh:targetClass biolink:Haplotype . + +biolink:Hospitalization a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], + sh:order 9 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], + 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:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 37 ; + sh:order 10 ; 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 23 ; - sh:path biolink:object_category_closure ] ; - sh:targetClass biolink:PhenotypicFeatureToDiseaseAssociation . - -biolink:PhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; - rdfs:subClassOf biolink:FeatureOrDiseaseQualifiersToEntityMixin ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:PhenotypicFeature ; - 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 IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; sh:order 11 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:double ; + sh:path biolink:deprecated ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:Hospitalization . + +biolink:HospitalizationOutcome a sh:NodeShape ; + sh:closed true ; + sh:description "An outcome resulting from an exposure event which is the increased manifestation of acute (e.g. emergency room visit) or chronic (inpatient) hospitalization." ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:HospitalizationOutcome . + +biolink:Human a sh:NodeShape ; + sh:closed true ; + sh:description "A member of the the species Homo sapiens." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:has_quotient ], - [ sh:datatype xsd:string ; - 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:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; sh:order 9 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:path biolink:full_name ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:description "Alternate human-readable names for a thing" ; sh:order 5 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:path biolink:synonym ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 10 ; + 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 "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 12 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A unique 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 13 ; - sh:path rdf:object ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:has_total ], - [ sh:datatype ; - 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:Literal ; - sh:order 10 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; sh:order 6 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism 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:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:has_count ] ; - sh:targetClass biolink:PhenotypicFeatureToEntityAssociationMixin . + sh:order 7 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:Human . -biolink:PhenotypicFeatureToPhenotypicFeatureAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; +biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; sh:closed true ; - sh:description "Association between two concept nodes of phenotypic character, qualified by the predicate used. This association may typically be used to specify 'similar_to' or 'member_of' relationships." ; + sh:description "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink: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:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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 3 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "used to 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 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:PhenotypicFeature ; - 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 28 ; + sh:path biolink:p_value ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - 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:timepoint ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdf:predicate ], + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is 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:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "used to 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:Literal ; - sh:order 45 ; - sh:path biolink:object_aspect_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 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 23 ; - sh:path biolink:object_category_closure ], + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource 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:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; + sh:order 33 ; sh:path rdf:type ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink: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 "Used to hold the 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:subject_category_closure ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype ; - 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:Literal ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ], + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - 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 19 ; - sh:path biolink:object_category ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; + sh:order 11 ; sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - 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:description "Used to hold 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:Literal ; - sh:order 47 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:has_count ], - [ 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:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; + sh:order 20 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ 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:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + 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:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 15 ; + 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:Literal ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + 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 32 ; - sh:path biolink:iri ], + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "used to 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:Literal ; - sh:order 43 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; + sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:has_total ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; + sh:order 3 ; sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - 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 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 28 ; + sh:order 27 ; sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an 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:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + 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 7 ; + 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 31 ; + 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 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "used to 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 "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ] ; - sh:targetClass biolink:PhenotypicFeatureToPhenotypicFeatureAssociation . + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + 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:InformationContentEntityToNamedThingAssociation . -biolink:PhenotypicQuality a sh:NodeShape ; - rdfs:subClassOf biolink:OrganismAttribute ; +biolink:Invertebrate a sh:NodeShape ; sh:closed true ; - sh:description "A property of a phenotype" ; + sh:description "An animal lacking a vertebral column. This group consists of 98% of all animal species." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - 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 value in this node property represents the knowledge provider that created or assembled the node 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:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_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 rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 5 ; - sh:path biolink:id ], + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; sh:order 9 ; + sh:path rdf:type ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; sh:path biolink:synonym ], - [ 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:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:iri ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + 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 7 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:path biolink:has_attribute ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; + sh:order 13 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ] ; - sh:targetClass biolink:PhenotypicQuality . + 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 8 ; + sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ] ; + sh:targetClass biolink:Invertebrate . -biolink:PhenotypicSex a sh:NodeShape ; - rdfs:subClassOf biolink:BiologicalSex ; +biolink:JournalArticle 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: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:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:datatype xsd:string ; + 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:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:creation_date ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 20 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:order 10 ; + sh:path dct:type ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:format ], + [ sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 0 ; + sh:path biolink:published_in ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 17 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 13 ; + sh:order 24 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 6 ; + sh:path biolink:summary ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path dct:description ], + sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + 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:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 1 ; + sh:path biolink:iso_abbreviation ], [ sh:datatype xsd:string ; - 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 value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 15 ; + sh:path biolink:provided_by ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 8 ; + 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:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], + sh:order 19 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; + sh:order 21 ; sh:path rdf:type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:full_name ], + [ 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:has_qualitative_value ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:iri ], + sh:path biolink:authors ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; + sh:description "keywords tagging a publication" ; + sh:order 7 ; + 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 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:path biolink:xref ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:order 22 ; + sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 23 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + 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:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 18 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:PhenotypicSex . - -biolink:PhysicalEssence a sh:NodeShape ; - rdfs:subClassOf biolink:PhysicalEssenceOrOccurrent ; - sh:closed false ; - sh:description "Semantic mixin concept. Pertains to entities that have physical properties such as mass, volume, or charge." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:PhysicalEssence . + 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:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 25 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + 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:targetClass biolink:JournalArticle . -biolink:PhysiologicalProcess a sh:NodeShape ; - rdfs:subClassOf biolink:BiologicalProcess ; +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:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; + sh:property [ sh:description "Alternate human-readable names for a thing" ; 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:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ], + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; + 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:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 0 ; + sh:order 8 ; 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:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 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:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 11 ; + sh:order 10 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + 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:in_taxon_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:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; + 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 4 ; - sh:path biolink:in_taxon ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 15 ; + sh:order 14 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:PhysiologicalProcess . + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ] ; + sh:targetClass biolink:LogOddsAnalysisResult . -biolink:Plant a sh:NodeShape ; - rdfs:subClassOf biolink:CellularOrganism ; +biolink:MacromolecularComplex a sh:NodeShape ; sh:closed true ; - sh:description "" ; + sh:description "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; + sh:order 2 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:nodeKind sh:Literal ; - sh:order 8 ; + sh:order 9 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 8 ; + 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 0 ; + sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ 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:minCount 1 ; - sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "Alternate human-readable names for a thing" ; 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:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; + sh:order 3 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 7 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ] ; + 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 "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:qualifiers ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 34 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 37 ; sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 36 ; 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 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ] ; - sh:targetClass biolink:Plant . - -biolink:PopulationToPopulationAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - sh:closed true ; - sh:description "An association between a two populations" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:datatype xsd:string ; sh:description "Used to hold 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:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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:datatype xsd:string ; sh:description "Used to hold 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:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "the population that form the subject of the association" ; + sh:description "Used to hold the 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 point in time" ; 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 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ 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:PopulationOfIndividualOrganisms ; - sh:description "the population that form the object of the association" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; 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 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - 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 17 ; - sh:path biolink:subject_category ], - [ 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:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:class biolink:BiologicalProcess ; + sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], + 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 7 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + 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 6 ; + sh:path biolink:publications ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 35 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - 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: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:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + 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 32 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink: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:class biolink:RetrievalSource ; - sh:description "A list of 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:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "used to 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:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:id ] ; - sh:targetClass biolink:PopulationToPopulationAssociation . - -biolink:PosttranslationalModification a sh:NodeShape ; - rdfs:subClassOf biolink:BiologicalEntity ; - 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:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ 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:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_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 biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An intermediate aggregator resource 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 22 ; + sh:path biolink:object_category_closure ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:minCount 1 ; sh:order 11 ; - sh:path dct:description ], + sh:path biolink:knowledge_level ] ; + 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:datatype xsd:string ; + sh:description "Used to hold the 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:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - 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:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "Used to hold the subject 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:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 6 ; + sh:order 30 ; sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:order 12 ; - sh:path biolink:has_attribute ], + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:description "Used to hold 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:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ] ; - sh:targetClass biolink:PosttranslationalModification . - -biolink:PreprintPublication a sh:NodeShape ; - rdfs:subClassOf biolink:Publication ; - 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:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "Used to hold 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:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], - [ 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 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:pages ], + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; + sh:order 37 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; - 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 "used to 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:Literal ; - sh:order 18 ; - sh:path rdfs:label ], + 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 32 ; + sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ 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:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an 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 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:keywords ], - [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:CellularComponent ; + sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path biolink:summary ], - [ sh:datatype xsd:string ; + sh:path rdf:object ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Publication ; + sh:description "One or more 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 dct:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + 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 7 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; + 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:Literal ; - sh:order 9 ; - sh:path biolink:format ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; + sh:nodeKind sh:IRI ; sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - 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 "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 14 ; - sh:path biolink:id ] ; - sh:targetClass biolink:PreprintPublication . - -biolink:ProcessRegulatesProcessAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - sh:closed true ; - sh:description "Describes a regulatory relationship between two genes or gene products." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:order 9 ; + 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 15 ; + sh:path biolink:original_predicate ], + [ 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 point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; @@ -22527,1227 +17436,1066 @@ biolink:ProcessRegulatesProcessAssociation a sh:NodeShape ; sh:order 21 ; sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh: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:maxCount 1 ; + sh:order 31 ; + 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 18 ; - 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 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object 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:MacromolecularMachineToCellularComponentAssociation . + +biolink:MacromolecularMachineToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:description "an association which has a macromolecular machine mixin as a subject" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ 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 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], + 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:targetClass biolink:MacromolecularMachineToEntityAssociationMixin . + +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 "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], [ 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:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 13 ; + 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 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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 11 ; - sh:path biolink:knowledge_level ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; 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:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ 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:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 15 ; + 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 22 ; - sh:path biolink:object_category_closure ], + 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:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:anyURI ; - 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:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], + 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 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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:datatype xsd:string ; sh:description "used to 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:Literal ; sh:order 16 ; sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold 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:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:BiologicalProcess ; - 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 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - 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:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ 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:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:class biolink:BiologicalProcess ; - 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:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ 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:IRI ; + sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 34 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ 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:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - 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:order 31 ; + 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 5 ; - sh:path biolink:qualifiers ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 30 ; - 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:targetClass biolink:ProcessRegulatesProcessAssociation . + sh:path biolink:agent_type ] ; + sh:targetClass biolink:MacromolecularMachineToMolecularActivityAssociation . -biolink:ProcessedMaterial a sh:NodeShape ; - rdfs:subClassOf biolink:ChemicalMixture ; +biolink:Mammal 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: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: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:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:is_supplement ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - 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 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "" ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:trade_name ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; - 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:description "The value in this node property represents the knowledge provider that created or assembled the node 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 1 ; - sh:path biolink:highest_FDA_approval_status ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 15 ; - sh:path biolink:category ], + 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 3 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; - sh:order 19 ; + sh:order 12 ; 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:datatype xsd:boolean ; - sh:description "" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 12 ; + sh:path biolink:iri ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; 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:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:iri ], + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 13 ; + sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdf:type ] ; - sh:targetClass biolink:ProcessedMaterial . + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:targetClass biolink:Mammal . -biolink:ProteinDomain a sh:NodeShape ; - rdfs:subClassOf biolink:BiologicalEntity ; +biolink:MappingCollection a sh:NodeShape ; + sh:closed false ; + sh:description "A collection of deprecated mappings." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:PredicateMapping ; + sh:description "A collection of relationships that are not used in biolink, but have biolink patterns that can be used to replace them. This is a temporary slot to help with the transition to the fully qualified predicate model in Biolink3." ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path biolink:predicate_mappings ] ; + sh:targetClass biolink:MappingCollection . + +biolink:MaterialSampleDerivationAssociation 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:description "An association between a material sample and the material entity from which it is derived." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh: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:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:path rdf:object ], + [ sh:class biolink:MaterialSample ; + sh:description "the material sample being described" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ], + sh:path rdf:subject ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 13 ; + sh:order 36 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category 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:Literal ; - sh:order 7 ; - 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 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ], + sh:description "Used to hold the 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:datatype xsd:string ; - sh:description "a human-readable description of an 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:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ] ; - sh:targetClass biolink:ProteinDomain . - -biolink:ProteinFamily a sh:NodeShape ; - rdfs:subClassOf biolink:BiologicalEntity ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - 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 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:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + 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 32 ; + sh:path biolink:category ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], + sh:description "Used to hold the subject 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:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the 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:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the 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 13 ; - 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:order 21 ; + 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 1 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], + sh:order 27 ; + 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 15 ; + sh:path biolink:original_predicate ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:ProteinFamily . - -biolink:ProteinIsoform a sh:NodeShape ; - rdfs:subClassOf biolink:Protein ; - 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:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 6 ; + sh:order 30 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:path biolink: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:Literal ; - 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 2 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; + sh:order 31 ; 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:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold 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 "derivation relationship" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 37 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ] ; - sh:targetClass biolink:ProteinIsoform . + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the 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:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ] ; + sh:targetClass biolink:MaterialSampleDerivationAssociation . -biolink:RNAProductIsoform a sh:NodeShape ; - rdfs:subClassOf biolink:RNAProduct ; +biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; - sh:description "Represents a protein that is a specific isoform of the canonical or reference RNA" ; + sh:description "An association between a material sample and a disease or phenotype." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; + 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:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - 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:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "Used to hold 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:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an 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:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; + sh:order 34 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:RNAProductIsoform . - -biolink:ReactionToCatalystAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:ReactionToParticipantAssociation ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the chemical element that is the target of the statement" ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:class biolink:MaterialSample ; + sh:description "the material sample being described" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 5 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_label_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:description "the side of a reaction being modeled (ie: left or right)" ; - sh:in ( "left" "right" ) ; + 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 18 ; + 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 2 ; - sh:path biolink:reaction_side ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - 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:datatype xsd:string ; sh:description "used to 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:Literal ; - sh:order 19 ; + sh:order 16 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; sh:order 36 ; - sh:path rdf:type ], + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink: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 24 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - 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:minCount 1 ; sh:order 30 ; - sh:path biolink:retrieval_source_ids ], + sh:path biolink:id ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 10 ; + sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink: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:class biolink:RetrievalSource ; + sh:description "A list of 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:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; sh:order 27 ; - sh:path biolink:object_namespace ], - [ 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:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:object_closure ], + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; + sh:order 37 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - 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 8 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:negated ], + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Used to hold 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:Literal ; - sh:order 26 ; + sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:integer ; - 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:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:stoichiometry ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource 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:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; + sh:order 8 ; 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:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; + sh:order 28 ; sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 22 ; + sh:order 19 ; sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - 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 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:Publication ; + sh:description "One or more 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:datatype xsd:string ; + sh:description "used to 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 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:Literal ; - sh:order 4 ; + 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 22 ; + sh:path biolink:object_category_closure ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; + sh:order 12 ; sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; + sh:order 13 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category 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 20 ; - sh:path biolink:subject_category ] ; - sh:targetClass biolink:ReactionToCatalystAssociation . + 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 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:datatype xsd:string ; + sh:description "Used to hold the subject 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:targetClass biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . -biolink:ReagentTargetedGene a sh:NodeShape ; - rdfs:subClassOf biolink:BiologicalEntity ; - 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." ; +biolink:MaterialSampleToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:description "An association between a material sample and something." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ 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:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + 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:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:MaterialSample ; + sh:description "the material sample being described" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:path rdf:subject ] ; + sh:targetClass biolink:MaterialSampleToEntityAssociationMixin . + +biolink:MicroRNA 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:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], + 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:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 1 ; + sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; + sh:order 11 ; sh:path dct:description ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 13 ; + 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 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:iri ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:path biolink:category ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ] ; - sh:targetClass biolink:ReagentTargetedGene . + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ] ; + sh:targetClass biolink:MicroRNA . -biolink:RelationshipType a sh:NodeShape ; - rdfs:subClassOf biolink:OntologyClass ; - sh:closed true ; - sh:description "An OWL property used as an edge label" ; +biolink:ModelToDiseaseAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:description "This mixin is used for any association class for which the subject (source node) plays the role of a 'model', in that it recapitulates some features of the disease in a way that is useful for studying the disease outside a patient carrying the disease" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "The relationship to the disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; + sh:description "The entity that serves as the model of the disease. This may be an organism, a strain of organism, a genotype or variant that exhibits similar features, or a gene that when mutated exhibits features of the disease" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; + sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:id ] ; - sh:targetClass biolink:RelationshipType . + sh:path rdf:subject ] ; + sh:targetClass biolink:ModelToDiseaseAssociationMixin . -biolink:RelativeFrequencyAnalysisResult a sh:NodeShape ; - rdfs:subClassOf biolink:StudyResult ; +biolink:MolecularActivityToChemicalEntityAssociation a sh:NodeShape ; sh:closed true ; - sh:description "A result of a relative frequency analysis." ; + 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:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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:datatype xsd:string ; + sh:description "Used to hold the subject 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:datatype xsd:string ; + sh:description "An intermediate aggregator resource 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:category ], + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + 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 27 ; + 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:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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 IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; + sh:description "Used to hold 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:Literal ; - sh:order 0 ; - sh:path biolink:license ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 14 ; + sh:order 36 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "used to 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:Literal ; - sh:order 2 ; - sh:path biolink:format ], + 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 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:description "used to 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:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - 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 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + 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 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; + sh:description "A unique identifier 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 high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:minCount 1 ; sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:path rdf:predicate ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 35 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:RelativeFrequencyAnalysisResult . - -biolink:SensitivityQuantifier a sh:NodeShape ; - rdfs:subClassOf biolink:RelationshipQuantifier ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:SensitivityQuantifier . - -biolink:SequenceVariantModulatesTreatmentAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - 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:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + 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 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + 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:nodeKind sh:Literal ; - sh:order 14 ; - 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:order 15 ; + 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:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + 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 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 6 ; + sh:path biolink:publications ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; + sh:path biolink:has_evidence ] ; + 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:datatype xsd:string ; sh:description "used to 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:Literal ; sh:order 16 ; sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - 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:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; sh:order 30 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 28 ; + sh:path biolink:p_value ], + [ 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 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:datatype xsd:string ; + sh:description "Used to hold the subject 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 human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:order 35 ; + 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 ; @@ -23757,27 +18505,25 @@ biolink:SequenceVariantModulatesTreatmentAssociation a sh:NodeShape ; [ sh:datatype xsd:string ; sh:description "Used to hold 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:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - 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:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + 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:object_category ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], + sh:order 36 ; + 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 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; @@ -23785,1321 +18531,1293 @@ biolink:SequenceVariantModulatesTreatmentAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:SequenceVariant ; - sh:description "variant that modulates the treatment of some disease" ; + [ 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:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object 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:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 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 22 ; + 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 31 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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:datatype xsd:string ; + sh:description "Used to hold 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 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:datatype xsd:string ; + sh:description "used to 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: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:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_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:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], + [ sh:datatype xsd:boolean ; + 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 18 ; + sh:path biolink:object_category ] ; + sh:targetClass biolink:MolecularActivityToMolecularActivityAssociation . + +biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Association that holds the relationship between a reaction and the pathway it participates in." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ 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:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; sh:order 33 ; sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "used to 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:datatype xsd:string ; + sh:description "Used to hold the 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 "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:datatype xsd:string ; + sh:description "A unique identifier 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:datatype xsd:string ; + sh:description "Used to hold the subject 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:datatype xsd:string ; + sh:description "Used to hold 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 17 ; + sh:path biolink:subject_category ], + [ 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:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Treatment ; - sh:description "treatment whose efficacy is modulated by the subject variant" ; + [ 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:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], + sh:order 34 ; + 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 27 ; 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:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 35 ; + 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 32 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource 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:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Pathway ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ] ; - sh:targetClass biolink:SequenceVariantModulatesTreatmentAssociation . - -biolink:Serial a sh:NodeShape ; - rdfs:subClassOf biolink:Publication ; - 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:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:pages ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:synonym ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; + sh:description "Used to hold 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:Literal ; - sh:order 12 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:rights ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 19 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; - sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; sh:order 7 ; - sh:path biolink:mesh_terms ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:issue ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh: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 3 ; - sh:path biolink:authors ], - [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:keywords ], + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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 dct:type ], + 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 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:MolecularActivity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 18 ; - sh:path biolink:iri ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:path biolink:object_category ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:creation_date ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ 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:datatype xsd:string ; + sh:description "used to 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: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:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 14 ; + sh:order 9 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path dct:description ], + sh:order 11 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:summary ], - [ sh:datatype xsd:string ; - sh:description "Should generally be set to an ontology class defined term for 'serial' or 'journal'." ; - sh:nodeKind sh:Literal ; sh:order 20 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - 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:path biolink:deprecated ], + [ 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, 'clinical approval status.'" ; + 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:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:volume ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], + sh:path biolink:highest_FDA_approval_status ], + [ 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:datatype xsd:string ; - 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 "" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; + sh:order 0 ; + sh:path biolink:is_supplement ], + [ 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 "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path dct:description ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 17 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Serials (journals) should have industry-standard identifier such as from ISSN." ; + sh:description "A unique 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:Literal ; - sh:order 17 ; + sh:order 13 ; sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ 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 "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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: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 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:has_attribute ], + sh:order 8 ; + sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:string ; + sh:order 16 ; + sh:path rdf:type ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 12 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - 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:description "" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:iso_abbreviation ] ; - sh:targetClass biolink:Serial . + sh:order 4 ; + sh:path biolink:trade_name ], + [ sh:datatype xsd:boolean ; + sh:description "" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:is_toxic ] ; + sh:targetClass biolink:MolecularMixture . -biolink:SeverityValue a sh:NodeShape ; - rdfs:subClassOf biolink:Attribute ; +biolink:MortalityOutcome a sh:NodeShape ; sh:closed true ; - sh:description "describes the severity of a phenotypic feature or disease" ; + sh:description "An outcome of death from resulting from an exposure event." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:targetClass biolink:MortalityOutcome . + +biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 39 ; + 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 36 ; + 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 32 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], + sh:order 6 ; + sh:path biolink:object_context_qualifier ], [ sh:datatype xsd:string ; - 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:Literal ; - sh:order 0 ; - 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 15 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 5 ; + sh:order 35 ; sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 38 ; + 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:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - 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 25 ; + sh:path biolink:object_closure ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:subject_closure ], + [ sh:class biolink: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:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "used to 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:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 19 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:description "Used to hold the biolink class/category 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 1 ; - sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 10 ; - sh:path biolink:category ] ; - sh:targetClass biolink:SeverityValue . - -biolink:SiRNA a sh:NodeShape ; - rdfs:subClassOf biolink:NoncodingRNAProduct ; - 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:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 22 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 28 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:description "Used to hold the object 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:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:synonym ], + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:description "used to 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:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 21 ; + 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 20 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 42 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - 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:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], + sh:order 8 ; + sh:path biolink:negated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 41 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; - sh:path biolink:category ] ; - sh:targetClass biolink:SiRNA . - -biolink:SmallMolecule a sh:NodeShape ; - rdfs:subClassOf biolink:MolecularEntity ; - 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:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 12 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an 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:nodeKind sh:Literal ; - sh:order 15 ; - sh:path dct:description ], + sh:order 13 ; + 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 27 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh: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:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:is_toxic ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:order 14 ; + 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 5 ; - sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:subject_context_qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:p_value ], + [ 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:Literal ; - sh:order 3 ; - sh:path biolink:max_tolerated_dose ], - [ 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:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdf:type ], + sh:order 7 ; + sh:path biolink:population_context_qualifier ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "indicates whether a molecular entity is a metabolite" ; + sh:order 1 ; + sh:path biolink:subject_aspect_qualifier ], + [ 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:nodeKind sh:Literal ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:is_metabolite ], + 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 37 ; + 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 10 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:deprecated ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 2 ; - sh:path biolink:available_from ], + sh:order 9 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh: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:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:trade_name ], + sh:order 29 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 30 ; + 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:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:SmallMolecule . + sh:order 3 ; + sh:path rdf:predicate ] ; + sh:targetClass biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . -biolink:Snv a sh:NodeShape ; - rdfs:subClassOf biolink:SequenceVariant ; +biolink:NoncodingRNAProduct 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:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 2 ; + sh:order 6 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; + sh:order 7 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Gene ; - sh:description "Each allele can be associated with any number of genes" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; + sh:order 3 ; + sh:path biolink:in_taxon_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:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; + sh:order 5 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The state of the sequence w.r.t a reference sequence" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:has_biological_sequence ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:Snv . + sh:order 12 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:NoncodingRNAProduct . -biolink:SocioeconomicExposure a sh:NodeShape ; - rdfs:subClassOf biolink:Attribute ; +biolink:NucleicAcidSequenceMotif 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: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:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + 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 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; + sh:order 13 ; sh:path biolink:deprecated ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ 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:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:order 7 ; + sh:path biolink:iri ], + [ 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:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:has_attribute_type ], + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + 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:datatype xsd:string ; sh:description "A unique 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:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - 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 "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:order 11 ; + sh:path dct:description ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:class biolink:SocioeconomicAttribute ; - sh:description "connects any entity to an attribute" ; + sh:path biolink:in_taxon_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:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:SocioeconomicExposure . - -biolink:SocioeconomicOutcome a sh:NodeShape ; - sh:closed true ; - sh:description "An general social or economic outcome, such as healthcare costs, utilization, etc., resulting from an exposure event" ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:SocioeconomicOutcome . + sh:order 8 ; + sh:path biolink:category ] ; + sh:targetClass biolink:NucleicAcidSequenceMotif . -biolink:Study a sh:NodeShape ; - rdfs:subClassOf biolink:Activity ; +biolink:NucleosomeModification a sh:NodeShape ; sh:closed true ; - sh:description "a detailed investigation and/or analysis" ; + 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:datatype xsd:string ; - 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 5 ; + 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:nodeKind sh:Literal ; sh:order 8 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 4 ; + sh:order 7 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:synonym ], + 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 "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ 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 11 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; + sh:order 14 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 6 ; + sh:path biolink:synonym ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:order 9 ; - sh:path dct:description ], + sh:path biolink:category ], + [ 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:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 6 ; - sh:path biolink:category ] ; - sh:targetClass biolink:Study . + sh:path biolink:in_taxon_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:NucleosomeModification . -biolink:StudyVariable a sh:NodeShape ; - rdfs:subClassOf biolink:InformationContentEntity ; +biolink:ObservedExpectedFrequencyAnalysisResult a sh:NodeShape ; sh:closed true ; - sh:description "a variable that is used as a measure in the investigation of a study" ; + sh:description "A result of a observed expected frequency analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:datatype xsd:string ; + sh:order 11 ; + 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 10 ; + sh:path biolink:category ], [ 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:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], + sh:order 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 8 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:description "Alternate human-readable names for a thing" ; sh:order 7 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:iri ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path biolink:creation_date ], + sh:path biolink:creation_date ] ; + sh:targetClass biolink:ObservedExpectedFrequencyAnalysisResult . + +biolink:Occurrent a sh:NodeShape ; + sh:closed false ; + sh:description "A processual entity." ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:Occurrent . + +biolink:OrganismAttribute a sh:NodeShape ; + sh:closed true ; + sh:description "describes a characteristic of an organismal 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: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 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + 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 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; + sh:order 14 ; sh:path biolink:deprecated ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - 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:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh: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 13 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:id ] ; - sh:targetClass biolink:StudyVariable . + sh:path biolink:full_name ] ; + sh:targetClass biolink:OrganismAttribute . -biolink:SubjectOfInvestigation a sh:NodeShape ; +biolink:OrganismTaxonToEntityAssociation a sh:NodeShape ; sh:closed false ; - sh:description "An entity that has the role of being studied in an investigation, study, or experiment" ; + sh:description "An association between an organism taxon and another entity" ; sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:SubjectOfInvestigation . + sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OrganismTaxon ; + sh:description "organism 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:targetClass biolink:OrganismTaxonToEntityAssociation . -biolink:TaxonToTaxonAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - sh:closed true ; +biolink:OrganismTaxonToEnvironmentAssociation a sh:NodeShape ; + sh:closed false ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - 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:datatype xsd:time ; - 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:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:description "predicate describing the relationship between the taxon and the environment" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ 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:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 12 ; + sh:path biolink:agent_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 32 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], + 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 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 36 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the 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:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ 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:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "used to 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 namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:class biolink:OrganismTaxon ; - sh:description "An association between individuals of different taxa." ; + sh:description "the taxon that is the subject of the association" ; 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:datatype xsd:string ; - sh:description "Used to hold 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:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 23 ; - 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 27 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; sh:order 30 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold 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:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; sh:order 26 ; 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:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 35 ; + 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 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ] ; - sh:targetClass biolink:TaxonToTaxonAssociation . - -biolink:TextMiningResult a sh:NodeShape ; - rdfs:subClassOf biolink:StudyResult ; - sh:closed true ; - sh:description "A result of text mining." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "Used to hold the 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:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 22 ; + 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:nodeKind sh:Literal ; - sh:order 9 ; + sh:order 31 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:description "Used to hold the 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:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the 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:NamedThing ; + sh:description "the environment in which the organism occurs" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:id ] ; - sh:targetClass biolink:TextMiningResult . + sh:path biolink:knowledge_source ] ; + sh:targetClass biolink:OrganismTaxonToEnvironmentAssociation . -biolink:ThingWithTaxon a sh:NodeShape ; +biolink:OrganismTaxonToOrganismTaxonAssociation a sh:NodeShape ; sh:closed false ; - sh:description "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" ; + sh:description "A relationship between two organism taxon nodes" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + 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:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_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:targetClass biolink:ThingWithTaxon . - -biolink:TranscriptToGeneRelationship a sh:NodeShape ; - rdfs:subClassOf biolink:SequenceFeatureRelationship ; - sh:closed true ; - sh:description "A gene is a collection of transcripts" ; - 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:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 36 ; sh:path biolink:has_attribute ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ 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 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; 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 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; sh:order 33 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "used to 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:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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:datatype xsd:string ; + sh:description "Used to hold 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:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; 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:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -25107,2624 +19825,2276 @@ biolink:TranscriptToGeneRelationship a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_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 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 34 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - 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:order 35 ; + sh:path dct:description ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OrganismTaxon ; + sh:description "organism taxon that is the subject of the association" ; 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:datatype xsd:string ; + sh:description "Used to hold the subject 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:description "Used to hold the 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 17 ; - sh:path biolink:subject_category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 22 ; + 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:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 31 ; + sh:path biolink:iri ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], [ 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:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:class biolink:Transcript ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh: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 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - 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: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 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - 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:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ] ; - sh:targetClass biolink:TranscriptToGeneRelationship . + sh:description "Used to hold the 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:OrganismTaxonToOrganismTaxonAssociation . -biolink:TranscriptionFactorBindingSite a sh:NodeShape ; - rdfs:subClassOf biolink:RegulatoryRegion ; - 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:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 9 ; - sh:path biolink:category ], +biolink:OrganismTaxonToOrganismTaxonInteraction a sh:NodeShape ; + sh:closed true ; + sh:description "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], + sh:order 10 ; + 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:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:description "An intermediate aggregator resource 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:datatype xsd:string ; - 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 object 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:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - 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 17 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + 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:Literal ; - sh:order 11 ; - sh:path rdfs:label ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; + sh:description "Used to hold 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:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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:order 5 ; + sh:path biolink:qualifier ], [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:description "the taxon that is the subject of the association" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], + 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 8 ; + 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 33 ; + 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 7 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - 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 20 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; + sh:order 38 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ] ; - sh:targetClass biolink:TranscriptionFactorBindingSite . - -biolink:VariantAsAModelOfDiseaseAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:VariantToDiseaseAssociation ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:SequenceVariant ; - sh:description "A variant that has a role in modeling the disease." ; + sh:order 29 ; + sh:path biolink:p_value ], + [ 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 "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:datatype xsd:anyURI ; - 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:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 6 ; + sh:path biolink:qualifiers ], [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; - sh:path biolink:agent_type ], + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; + sh:order 21 ; 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 28 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 15 ; + 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 32 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 36 ; 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 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - 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 27 ; - 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:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ 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 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + 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:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 16 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; + sh:minCount 1 ; sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:path biolink:id ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "the environment in which the two taxa interact" ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:order 0 ; + sh:path biolink:associated_environmental_context ], + [ sh:datatype xsd:string ; + sh:description "Used to hold 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:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 25 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 23 ; + sh:path biolink:object_category_closure ] ; + 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:datatype xsd:string ; + sh:description "Used to hold the 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:datatype xsd:string ; - sh:description "used to 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:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; 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:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 36 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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:datatype xsd:string ; sh:description "used to 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:Literal ; sh:order 16 ; sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "Used to hold 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:Literal ; - sh:order 38 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 23 ; + 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 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "An intermediate aggregator resource 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:datatype xsd:string ; + sh:description "Used to hold 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 39 ; - sh:path biolink:subject_direction_qualifier ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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 unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:minCount 1 ; + sh:order 30 ; + 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 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 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "used to 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:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 14 ; + 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 21 ; sh:path biolink:subject_category_closure ], + [ sh:class biolink:OrganismTaxon ; + sh:description "the more specific taxon" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OrganismTaxon ; + sh:description "the more general taxon" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The relationship to the disease" ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + 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:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ 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 7 ; - sh:path biolink:has_evidence ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ 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:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:qualified_predicate ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ] ; - sh:targetClass biolink:VariantAsAModelOfDiseaseAssociation . - -biolink:VariantToEntityAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - 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:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated with some other entity" ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; - sh:targetClass biolink:VariantToEntityAssociationMixin . + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ] ; + sh:targetClass biolink:OrganismTaxonToOrganismTaxonSpecialization . -biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:VariantToGeneAssociation ; +biolink:OrganismToOrganismAssociation 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 "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - 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:nodeKind sh:IRI ; - sh:order 6 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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 "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:iri ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:timepoint ], + sh:order 34 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; + sh:description "Used to hold 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 1 ; - sh:path biolink:expression_site ], + sh:order 36 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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 19 ; + 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:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; + sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 31 ; + 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 10 ; + sh:order 6 ; sh:path biolink:publications ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated with some other entity" ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 32 ; + sh:path biolink:category ], + [ 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:nodeKind sh:IRI ; - sh:order 4 ; + sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "used to 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:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of 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 37 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ 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:retrieval_source_ids ], + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Optional quantitative value indicating degree of expression." ; + sh:description "An intermediate aggregator resource 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:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:quantifier_qualifier ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path biolink:phenotypic_state ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - 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 9 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], + sh:path biolink:negated ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 16 ; + sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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:datatype xsd:string ; + sh:description "Used to hold 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:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 25 ; + sh:order 21 ; sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], - [ sh:class biolink:LifeStage ; - sh:description "stage during which gene or protein expression of takes place." ; + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], + [ sh:class biolink:IndividualOrganism ; + sh:description "An association between two individual organisms." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path biolink:stage_qualifier ], + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink: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 26 ; + sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ 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:Literal ; - sh:order 5 ; + sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - 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:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:order 35 ; + 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 22 ; - sh:path biolink:object_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - 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 11 ; - sh:path biolink:has_evidence ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "used to 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:Literal ; - sh:order 41 ; - sh:path biolink:deprecated ], + 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 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_object ] ; - sh:targetClass biolink:VariantToGeneExpressionAssociation . + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ] ; + sh:targetClass biolink:OrganismToOrganismAssociation . -biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; +biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - 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:property [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 34 ; + sh:path 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:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; + sh:order 12 ; sh:path biolink:agent_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:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:order 33 ; - sh:path biolink:category ], + 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 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 4 ; + sh:path biolink: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 43 ; + sh:path biolink:frequency_qualifier ], + [ 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:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 46 ; + sh:order 41 ; sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the 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:datatype xsd:string ; + sh:description "Used to hold 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:Literal ; - sh:order 42 ; - sh:path biolink:has_percentage ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path biolink:subject_direction_qualifier ], + [ 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:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - 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:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; + sh:order 37 ; sh:path biolink:deprecated ], + [ 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:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; + sh:order 38 ; sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_direction_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 19 ; - 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 8 ; - sh:path biolink:has_evidence ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 37 ; + sh:order 36 ; sh:path biolink:has_attribute ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:boolean ; + 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:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:RetrievalSource ; sh:description "A list of 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:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:double ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_quotient ], + sh:order 13 ; + 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:datatype xsd:string ; - sh:description "used to 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 "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], + sh:order 40 ; + sh:path biolink:object_aspect_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:datatype xsd:string ; + sh:description "Used to hold the 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 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:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 10 ; + sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 6 ; + sh: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 32 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier 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:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:has_total ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + 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 42 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold 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:Literal ; - sh:order 24 ; + sh:order 23 ; sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 17 ; - sh:path biolink:original_object ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], + sh:order 28 ; + sh:path biolink:p_value ] ; + sh:targetClass biolink:OrganismalEntityAsAModelOfDiseaseAssociation . + +biolink:PairwiseGeneToGeneInteraction a sh:NodeShape ; + sh:closed true ; + sh:description "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:RetrievalSource ; + sh:description "A list of 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 original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:Publication ; sh:description "One or more 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:order 6 ; sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "A unique identifier 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:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype ; - 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 biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "used to 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:Literal ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], + sh:order 16 ; + 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:description "Used to hold the 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:object_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource 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:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - 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:description "Used to hold the 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:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:qualified_predicate ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:time ; - 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:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:timepoint ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:has_count ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated in some way with the phenotype state" ; + sh:path biolink:object_category ], + [ 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:class biolink:OntologyClass ; - sh:description "Used to hold the 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 34 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; + sh:order 33 ; sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ] ; - sh:targetClass biolink:VariantToPhenotypicFeatureAssociation . - -biolink:VariantToPopulationAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - 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:datatype xsd:double ; - sh:description "frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency" ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:has_percentage ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "used to 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 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:Literal ; - sh:order 19 ; - sh:path biolink:original_subject ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "interaction relationship type" ; + 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 36 ; + 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 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; + sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - 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 subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_predicate ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:p_value ], + sh:order 35 ; + 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 22 ; + 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 11 ; - sh:path biolink:publications ], - [ sh:datatype xsd:integer ; - sh:description "number all populations that carry a particular allele, aka allele number" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:has_total ], [ sh:datatype xsd:string ; - 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 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:Literal ; - sh:order 35 ; - sh:path biolink:id ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdfs:label ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "the population that is observed to have the frequency" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + 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:nodeKind sh:Literal ; - sh:order 36 ; + sh:order 31 ; sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 29 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:SequenceVariant ; - sh:description "an allele that has a certain frequency in a given population" ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ 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:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ] ; + 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:datatype xsd:string ; + sh:description "Used to hold the object 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:RetrievalSource ; + sh:description "A list of 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:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 7 ; - sh:path biolink:frequency_qualifier ], + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource 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:datatype xsd:string ; + sh:description "used to 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:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Used to hold 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 17 ; - sh:path biolink:agent_type ], + sh:order 25 ; + sh:path biolink:object_namespace ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 16 ; + sh:order 12 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:description "interaction relationship type" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:minCount 1 ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], + sh:order 5 ; + sh:path biolink: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: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 41 ; - 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 16 ; + sh:path biolink:original_predicate ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 36 ; + 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 10 ; + sh:order 6 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - 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 biolink class/category 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:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 23 ; + sh:order 19 ; sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 38 ; + sh:order 34 ; 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 26 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 14 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:integer ; - sh:description "number in object population that carry a particular allele, aka allele count" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_closure ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:interacting_molecules_category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "Used to hold 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:Literal ; - sh:order 28 ; + sh:order 24 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:qualifier ], + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + 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:datatype xsd:string ; sh:description "used to 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:Literal ; - sh:order 21 ; + sh:order 17 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:aggregator_knowledge_source ] ; - sh:targetClass biolink:VariantToPopulationAssociation . - -biolink:Vertebrate a sh:NodeShape ; - rdfs:subClassOf biolink:CellularOrganism ; - sh:closed true ; - sh:description "A sub-phylum of animals consisting of those having a bony or cartilaginous vertebral column." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; + sh:description "Used to hold the 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 "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 33 ; sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 8 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ] ; - sh:targetClass biolink:Vertebrate . - -biolink:Virus a sh:NodeShape ; - rdfs:subClassOf biolink:OrganismalEntity ; - 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:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "identifier for the interaction. This may come from an interaction database such as IMEX." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; + sh:order 31 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + [ 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:nodeKind sh:Literal ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:path rdf:subject ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 32 ; + 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 22 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 38 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism 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 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 7 ; + sh:path biolink:publications ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the subject 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: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:nodeKind sh:Literal ; - 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 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; - sh:path biolink:category ] ; - sh:targetClass biolink:Virus . + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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:targetClass biolink:PairwiseMolecularInteraction . -biolink:WebPage a sh:NodeShape ; - rdfs:subClassOf biolink:Publication ; +biolink:Patent 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: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:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:rights ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:deprecated ], + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:order 6 ; + sh:path dct:type ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 13 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:provided_by ], + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:iri ], + sh:order 9 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], + sh:order 17 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; + sh:order 3 ; + sh:path biolink:keywords ], [ sh:datatype xsd:string ; 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:nodeKind sh:Literal ; 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:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:keywords ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:mesh_terms ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path dct:description ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:full_name ], - [ 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:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:summary ], - [ sh:datatype xsd:string ; - 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 "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:nodeKind sh:Literal ; sh:order 18 ; sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path dct:type ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:format ] ; - sh:targetClass biolink:WebPage . - -biolink:Activity a sh:NodeShape ; - rdfs:subClassOf biolink:NamedThing ; - 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:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:order 21 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 10 ; + sh:order 20 ; 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 16 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - 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 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:nodeKind sh:Literal ; - sh:order 5 ; + sh:order 15 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - 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 "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; + sh:order 19 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:Activity . + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:rights ] ; + sh:targetClass biolink:Patent . -biolink:AdministrativeEntity a sh:NodeShape ; - rdfs:subClassOf biolink:NamedThing ; +biolink:PathognomonicityQuantifier a sh:NodeShape ; sh:closed false ; + sh:description "A relationship quantifier between a variant or symptom and a disease, which is high when the presence of the feature implies the existence of the disease" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; + sh:targetClass biolink:PathognomonicityQuantifier . + +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 "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; + sh:order 15 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:path biolink:timepoint ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; + sh:order 9 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; sh:order 6 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; + sh:path biolink:id ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; sh:order 3 ; - sh:path biolink:synonym ], + 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:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 10 ; + sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - 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 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:minCount 1 ; - sh:nodeKind sh:Literal ; + 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:id ] ; - sh:targetClass biolink:AdministrativeEntity . + sh:path biolink:has_qualitative_value ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:category ], + [ 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:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 7 ; + sh:path biolink:provided_by ] ; + sh:targetClass biolink:PathologicalAnatomicalExposure . -biolink:Annotation a sh:NodeShape ; - sh:closed false ; - sh:description "Biolink Model root class for entity annotations." ; +biolink:PathologicalAnatomicalOutcome a sh:NodeShape ; + sh:closed true ; + sh:description "An outcome resulting from an exposure event which is the manifestation of an abnormal anatomical structure." ; sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:Annotation . + sh:targetClass biolink:PathologicalAnatomicalOutcome . -biolink:Article a sh:NodeShape ; - rdfs:subClassOf biolink:Publication ; +biolink:PathologicalAnatomicalStructure a sh:NodeShape ; sh:closed true ; - sh:description "a piece of writing on a particular topic presented as a stand-alone section of a larger publication" ; + sh: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:datatype xsd:string ; + sh:property [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path biolink:license ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + sh:path dct:description ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:summary ], - [ 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:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:keywords ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:mesh_terms ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:format ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 21 ; + sh:order 9 ; sh:path rdf:type ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:creation_date ], + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:issue ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:pages ], - [ sh:datatype xsd:string ; - sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; + sh:path biolink:has_attribute ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:iso_abbreviation ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 22 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path dct:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 9 ; + sh:path biolink:in_taxon_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:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:volume ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; + sh:order 7 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; + [ sh:datatype xsd:string ; + sh:description "A unique 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:Literal ; + 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:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:published_in ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 20 ; - sh:path biolink:category ] ; - sh:targetClass biolink:Article . + sh:path biolink:in_taxon ] ; + sh:targetClass biolink:PathologicalAnatomicalStructure . -biolink:Behavior a sh:NodeShape ; - rdfs:subClassOf biolink:BiologicalProcess ; +biolink:PathologicalEntityMixin a sh:NodeShape ; + sh:closed false ; + sh:description "A pathological (abnormal) structure or process." ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:PathologicalEntityMixin . + +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:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; 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: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:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 16 ; + sh:path biolink:deprecated ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; sh:order 11 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 output of the process" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_output ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], [ 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:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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: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 "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:Behavior . + 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: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 "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path dct:description ] ; + sh:targetClass biolink:PathologicalProcess . -biolink:BehavioralFeature a sh:NodeShape ; - rdfs:subClassOf biolink:PhenotypicFeature ; +biolink:PathologicalProcessExposure a sh:NodeShape ; sh:closed true ; - sh:description "A phenotypic feature which is behavioral in nature." ; + 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:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + 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:nodeKind sh:Literal ; - sh:order 10 ; + 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:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; + 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:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 15 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; + 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:datatype xsd:string ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; 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 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 10 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:BehavioralFeature . + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:targetClass biolink:PathologicalProcessExposure . -biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; +biolink:PathologicalProcessOutcome 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:description "An outcome resulting from an exposure event which is the manifestation of a pathological process." ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:PathologicalProcessOutcome . + +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:datatype xsd:string ; - sh:description "used to 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 7 ; + sh:path rdf:type ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + sh:order 9 ; + sh:path dct:description ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 6 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:anyURI ; - 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 unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + 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:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the 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 "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:order 5 ; - sh:path biolink: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:path biolink:iri ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ] ; + sh:targetClass biolink:Phenomenon . + +biolink:PhenotypicFeatureToDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:has_total ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], + 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 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "used to 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:Literal ; - sh:order 16 ; + sh:order 17 ; sh:path biolink:original_object ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 43 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; + sh:order 30 ; sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - 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 26 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + 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:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 47 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:order 29 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; + sh:order 27 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an 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 48 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:PhenotypicFeature ; + 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 36 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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 1 ; + sh:path rdf:subject ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:has_quotient ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 44 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + 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:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 2 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], + sh:order 39 ; + sh:path biolink:has_count ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; + sh:order 4 ; sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - 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 27 ; - 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:order 23 ; + 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:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 16 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:description "Used to hold 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:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:path biolink:object_namespace ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 30 ; + sh:order 31 ; sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 33 ; + sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ 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:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; + sh:description "Used to hold the 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:object_closure ] ; - sh:targetClass biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . - -biolink:CellularComponent a sh:NodeShape ; - rdfs:subClassOf biolink:AnatomicalEntity ; - sh:closed true ; - sh:description "A location in or around a cell" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:path biolink:subject_closure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 38 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; + sh:order 45 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 32 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an 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 9 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold 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:Literal ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource 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 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:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; 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 12 ; - sh:path biolink:has_attribute ], + sh:path rdf:object ], [ sh:datatype xsd:string ; - 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 object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the 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:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:knowledge_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 18 ; + 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 8 ; + 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 7 ; + 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 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:path biolink:qualifiers ] ; + sh:targetClass biolink:PhenotypicFeatureToDiseaseAssociation . + +biolink:PhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ 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 13 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; + 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 9 ; - sh:path rdf:type ], + sh:path biolink:qualified_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 12 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:has_count ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:path biolink:has_percentage ], + [ 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:frequency_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:has_total ], + [ sh:class biolink:PhenotypicFeature ; + 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:Literal ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path rdf:subject ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; sh:order 8 ; - sh:path biolink:category ] ; - sh:targetClass biolink:CellularComponent . + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:object_aspect_qualifier ] ; + sh:targetClass biolink:PhenotypicFeatureToEntityAssociationMixin . -biolink:ChemicalExposure a sh:NodeShape ; - rdfs:subClassOf biolink:Attribute ; +biolink:PhenotypicFeatureToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; - sh:description "A chemical exposure is an intake of a particular chemical entity." ; + sh:description "Association between two concept nodes of phenotypic character, qualified by the predicate used. This association may typically be used to specify 'similar_to' or 'member_of' relationships." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:property [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 42 ; + sh:path biolink:has_percentage ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 36 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - 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 "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:Literal ; - sh:order 2 ; - sh:path rdfs:label ], + sh:order 16 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 35 ; + 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 23 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; + sh:order 38 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "Used to hold 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:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 6 ; + sh:order 31 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:synonym ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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:datatype xsd:string ; + sh:description "used to 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 4 ; - sh:path biolink:has_qualitative_value ], + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_attribute_type ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 45 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:timepoint ], + sh:order 29 ; + sh:path biolink:p_value ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 14 ; + sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ] ; - sh:targetClass biolink:ChemicalExposure . - -biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - 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:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 31 ; - sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:order 9 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - 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 21 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:qualifiers ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:has_quotient ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ], + sh:order 13 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_closure ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold 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 "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 33 ; + sh:path biolink:category ], + [ sh:class biolink:PhenotypicFeature ; + 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 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 23 ; - sh:path biolink:object_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:description "A 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 12 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:order 44 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:anyURI ; - 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 "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 43 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 40 ; + 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 ; @@ -27732,151 +22102,108 @@ biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:No sh:order 18 ; sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "" ; - sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; + sh:order 48 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:FDA_adverse_event_level ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - 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 7 ; - sh:path biolink:publications ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 46 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to 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 "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + 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:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdf:predicate ], + sh:order 47 ; + sh:path biolink:qualified_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:class biolink:OntologyClass ; sh:description "Used to hold the 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:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 28 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - 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: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 19 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - 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 8 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_label_closure ] ; - sh:targetClass biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . + sh:order 30 ; + sh:path biolink:adjusted_p_value ] ; + sh:targetClass biolink:PhenotypicFeatureToPhenotypicFeatureAssociation . -biolink:ClinicalCourse a sh:NodeShape ; - rdfs:subClassOf biolink:ClinicalAttribute ; +biolink:PhenotypicQuality 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:description "A property of a phenotype" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - 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 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier 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 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:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:class biolink:NamedThing ; + sh: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:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -27884,2760 +22211,2782 @@ biolink:ClinicalCourse a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - 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:Literal ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], + sh:order 8 ; + sh:path biolink:full_name ] ; + 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 "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], [ 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:datatype xsd:string ; - sh:description "A unique 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:Literal ; - 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 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:datatype xsd:string ; - 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 6 ; + sh:path biolink:provided_by ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path dct:description ] ; - sh:targetClass biolink:ClinicalCourse . - -biolink:ClinicalIntervention a sh:NodeShape ; - rdfs:subClassOf biolink:ClinicalEntity ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; + sh:order 14 ; sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], + [ 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:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 7 ; + sh:order 11 ; sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; + [ 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:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:path biolink:iri ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ] ; - sh:targetClass biolink:ClinicalIntervention . + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ] ; + sh:targetClass biolink:PhenotypicSex . + +biolink:PhysicalEssence a sh:NodeShape ; + sh:closed false ; + sh:description "Semantic mixin concept. Pertains to entities that have physical properties such as mass, volume, or charge." ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:PhysicalEssence . + +biolink:PhysicalEssenceOrOccurrent a sh:NodeShape ; + sh:closed false ; + sh:description "Either a physical or processual entity." ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:PhysicalEssenceOrOccurrent . -biolink:Dataset a sh:NodeShape ; - rdfs:subClassOf biolink:InformationContentEntity ; +biolink:PhysiologicalProcess 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:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 8 ; + sh:order 0 ; sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 12 ; + sh:path rdf:type ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 13 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 rdf:type ], + 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 10 ; + 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:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink: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 human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:order 14 ; + 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 4 ; + sh:path biolink:in_taxon ], + [ sh:description "Alternate human-readable names for a thing" ; sh:order 9 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; + sh:path biolink:synonym ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:order 5 ; - sh:path biolink:xref ] ; - sh:targetClass biolink:Dataset . + sh:path biolink:in_taxon_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: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:targetClass biolink:PhysiologicalProcess . -biolink:DatasetDistribution a sh:NodeShape ; - rdfs:subClassOf biolink:InformationContentEntity ; +biolink:PlanetaryEntity a sh:NodeShape ; sh:closed true ; - sh:description "an item that holds distribution level information about a dataset." ; + sh:description "Any entity or process that exists at the level of the whole planet" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:license ], + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; + sh:order 7 ; sh:path rdf:type ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - 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 6 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; + sh:order 11 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:full_name ], + sh:order 9 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 9 ; + sh:order 4 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; + sh:order 5 ; sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:distribution_download_url ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; + sh:order 0 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:DatasetDistribution . + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], + [ 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:PlanetaryEntity . -biolink:Device a sh:NodeShape ; - rdfs:subClassOf biolink:NamedThing ; +biolink:Plant 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:description "" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 9 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; + sh:order 4 ; + 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: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:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; + sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + [ sh:description "Alternate human-readable names for a thing" ; sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; - sh:order 10 ; + sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ] ; - sh:targetClass biolink:Device . + sh:order 1 ; + sh:path biolink:in_taxon_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. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:DrugExposure a sh:NodeShape ; - rdfs:subClassOf biolink:ChemicalExposure ; +biolink:Polypeptide a sh:NodeShape ; sh:closed true ; - sh:description "A drug exposure is an intake of a particular drug." ; + 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:datatype xsd:string ; sh:description "A unique 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:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ 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 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - 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:Literal ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 rdfs:label ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:order 10 ; - sh:path biolink:synonym ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 1 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; + 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: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 3 ; - sh:path biolink:has_attribute_type ], + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; + sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ 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:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:description "Alternate human-readable names for a thing" ; sh:order 5 ; - sh:path biolink:iri ], + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 14 ; + sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 11 ; - sh:path biolink:category ] ; - sh:targetClass biolink:DrugExposure . + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ 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:Polypeptide . -biolink:EnvironmentalExposure a sh:NodeShape ; - rdfs:subClassOf biolink:Attribute ; +biolink:PopulationToPopulationAssociation 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:description "An association between a two populations" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - 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 36 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - 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 "used to 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:Literal ; - sh:order 1 ; - sh:path rdfs:label ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 6 ; + sh:order 30 ; sh:path biolink:id ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], + [ sh:description "A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + 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:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "Used to hold the object 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:Literal ; - 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 14 ; - sh:path biolink:has_attribute ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "the population that form the object of the association" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:boolean ; + 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:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], + sh:description "Used to hold the 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:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:order 9 ; + 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 32 ; + sh:path biolink:category ], + [ 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 31 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + 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:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the 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 biolink:has_attribute_type ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:EnvironmentalExposure . - -biolink:Exon a sh:NodeShape ; - rdfs:subClassOf biolink:BiologicalEntity ; - 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:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 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 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:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "Used to hold 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:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - 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 33 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "used to 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:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; + sh:description "Used to hold the subject 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: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:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], + [ sh: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 3 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], [ 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:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ 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:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ] ; - sh:targetClass biolink:Exon . + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ] ; + sh:targetClass biolink:PosttranslationalModification . -biolink:FeatureOrDiseaseQualifiersToEntityMixin a sh:NodeShape ; - rdfs:subClassOf biolink:FrequencyQualifierMixin ; - sh:closed false ; - sh:description "Qualifiers for disease or phenotype to entity associations." ; +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:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:property [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path rdf:object ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink: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 "mesh terms tagging a publication" ; + sh:order 4 ; + sh:path biolink:mesh_terms ], + [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; sh:order 6 ; - sh:path rdf:subject ], + sh:path dct:type ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + 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:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:predicate ], + sh:order 14 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 19 ; + sh:path dct:description ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:frequency_qualifier ] ; - sh:targetClass biolink:FeatureOrDiseaseQualifiersToEntityMixin . - -biolink:GeneFamily a sh:NodeShape ; - rdfs:subClassOf biolink:BiologicalEntity ; - sh:closed true ; - sh:description "any grouping of multiple genes or gene products related by common descent" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; sh:order 3 ; - sh:path biolink:provided_by ], + sh:path biolink:keywords ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + 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 "Alternate human-readable names for a thing" ; + sh:order 13 ; + sh:path biolink:synonym ], + [ 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:nodeKind sh:Literal ; - sh:order 11 ; + sh:order 18 ; sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:order 17 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 13 ; + sh:order 20 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - 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 15 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:iri ], + 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 16 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:license ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:summary ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:format ] ; + sh:targetClass biolink:PreprintPublication . + +biolink:ProcessRegulatesProcessAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Describes a regulatory relationship between two genes or gene products." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; + 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:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 7 ; + sh:order 30 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "Used to hold 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:Literal ; - sh:order 2 ; - sh:path biolink:in_taxon_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:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an 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:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:BiologicalProcess ; + 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 0 ; - sh:path biolink:has_gene_or_gene_product ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 9 ; - sh:path biolink:category ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "Used to hold the object 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:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "Used to hold 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:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:GeneFamily . - -biolink:GeneticInheritance a sh:NodeShape ; - rdfs:subClassOf biolink:BiologicalEntity ; - 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:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 23 ; + 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:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:order 31 ; + 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:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 36 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 "Used to hold the biolink class/category of an association. This is 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:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "used to 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:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ 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:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 37 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; + sh:order 35 ; 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:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:BiologicalProcess ; + 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:nodeKind sh:Literal ; + sh:minCount 1 ; + 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 32 ; + sh:path biolink:category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; sh:order 7 ; - sh:path biolink:iri ], + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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:datatype xsd:string ; + sh:description "An intermediate aggregator resource 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 rdfs:label ] ; - sh:targetClass biolink:GeneticInheritance . - -biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - 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:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh: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:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ] ; + sh:targetClass biolink:ProcessRegulatesProcessAssociation . + +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: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, 'clinical approval status.'" ; + 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:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], + sh:order 16 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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 "" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 4 ; + sh:path biolink:trade_name ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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 21 ; - sh:path biolink:subject_category_closure ], + sh:order 20 ; + sh:path biolink:deprecated ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 10 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 36 ; + sh:order 19 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:boolean ; + sh:description "" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 7 ; + sh:path biolink:is_toxic ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 18 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:Genotype ; - sh:description "a genotype that is associated in some way with a disease state" ; + 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:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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: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 0 ; - sh:path rdf:subject ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + 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 39 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to 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 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 12 ; + sh:path biolink:synonym ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 11 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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 "" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh: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:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 0 ; + sh:path biolink:is_supplement ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 13 ; + sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 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: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:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:path biolink:has_attribute ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 3 ; + sh:path biolink:in_taxon_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 long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; + sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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 7 ; + sh:path biolink:iri ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 11 ; + sh:path dct:description ], + [ 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 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; + 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 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:qualified_predicate ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:datatype xsd:string ; - sh:description "E.g. is pathogenic for" ; + sh:description "A unique 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:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:anyURI ; - 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 6 ; + sh:path biolink:id ] ; + sh:targetClass biolink:Protein . + +biolink:ProteinDomain a sh:NodeShape ; + sh:closed true ; + sh:description "A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh: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:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 12 ; + sh:path dct:description ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 6 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 14 ; + sh:path biolink:deprecated ], + [ 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:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:path rdf:type ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh: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 2 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 30 ; + sh:order 7 ; sh:path biolink:id ], - [ sh:class biolink:Disease ; - sh:description "a disease that is associated with that genotype" ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:order 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. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:ProteinDomain . + +biolink:ProteinFamily a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:frequency_qualifier ], + 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:datatype xsd:string ; - sh:description "Used to hold 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 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:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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:order 5 ; + 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 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 biolink:in_taxon_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 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:GenotypeToDiseaseAssociation . - -biolink:GeographicLocation a sh:NodeShape ; - rdfs:subClassOf biolink:PlanetaryEntity ; - sh:closed true ; - sh:description "a location that can be described in lat/long coordinates" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 1 ; + sh:path biolink:in_taxon ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 6 ; + sh:path biolink:synonym ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; + sh:order 8 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 6 ; + sh:order 7 ; sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 13 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - 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 3 ; + sh:path biolink:provided_by ] ; + 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:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "latitude" ; + [ sh:datatype xsd:string ; + 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 1 ; + sh:path biolink:xref ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:latitude ], - [ sh:datatype xsd:float ; - sh:description "longitude" ; + sh:order 11 ; + sh:path dct:description ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:longitude ], + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an 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:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; + sh:order 4 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; - sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:GeographicLocation . - -biolink:Mammal a sh:NodeShape ; - rdfs:subClassOf biolink:CellularOrganism ; - 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:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:path biolink:deprecated ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; + sh:order 5 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - 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:order 2 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:ProteinIsoform . + +biolink:RNAProduct 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:datatype xsd:string ; sh:description "A unique 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:Literal ; sh:order 6 ; sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ 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:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 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:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:category ] ; - sh:targetClass biolink:Mammal . + sh:path biolink:category ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:full_name ] ; + sh:targetClass biolink:RNAProduct . -biolink:MolecularMixture a sh:NodeShape ; - rdfs:subClassOf biolink:ChemicalMixture ; +biolink:RNAProductIsoform 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:description "Represents a protein that is a specific isoform of the canonical or reference RNA" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ 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:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdfs:label ], - [ 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, 'clinical approval status.'" ; - 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 1 ; - sh:path biolink:highest_FDA_approval_status ], + sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 13 ; + sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh: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 "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:path biolink:in_taxon_label ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "" ; + sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:is_supplement ], - [ sh:datatype xsd:string ; - 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:order 7 ; + sh:path biolink:iri ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; sh:order 5 ; - sh:path biolink:available_from ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; + 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:synonym ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - 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 8 ; - sh:path biolink:has_chemical_role ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - 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 13 ; + sh:path biolink:deprecated ], + [ 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 biolink:drug_regulatory_status_world_wide ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:trade_name ], + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 15 ; - sh:path biolink:category ] ; - sh:targetClass biolink:MolecularMixture . - -biolink:Occurrent a sh:NodeShape ; - rdfs:subClassOf biolink:PhysicalEssenceOrOccurrent ; - sh:closed false ; - sh:description "A processual entity." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:Occurrent . + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ] ; + sh:targetClass biolink:RNAProductIsoform . -biolink:Onset a sh:NodeShape ; - rdfs:subClassOf biolink:ClinicalCourse ; +biolink:ReactionToCatalystAssociation a sh:NodeShape ; sh:closed true ; - sh:description "The age group in which (disease) symptom manifestations appear." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object label 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: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:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:path biolink:reaction_side ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 14 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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_closure ], + [ sh:datatype xsd:string ; + sh:description "used to 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 19 ; + 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 1 ; - sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; + sh:order 38 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - 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 "Used to hold the subject 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:subject_label_closure ], [ sh:datatype xsd:string ; - 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 "Used to hold 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:Literal ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:order 26 ; + 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 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 20 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:minCount 1 ; + sh:order 33 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - 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 23 ; + sh:path biolink:object_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], + sh:order 37 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:Onset . - -biolink:OrganismAttribute a sh:NodeShape ; - rdfs:subClassOf biolink:Attribute ; - sh:closed true ; - sh:description "describes a characteristic of an organismal entity." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; sh:order 12 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - 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:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 31 ; + sh:path biolink:p_value ], + [ 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 18 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + 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:GeneOrGeneProduct ; + sh:description "the chemical element that is the target of the statement" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 5 ; + sh:path rdf:object ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Publication ; + sh:description "One or more 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 "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:has_attribute_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:path biolink:reaction_direction ], + [ sh:datatype xsd:integer ; + 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:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], + sh:order 0 ; + sh:path biolink:stoichiometry ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 36 ; + 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 35 ; + sh:path biolink:category ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 40 ; + sh:path biolink:deprecated ], + [ 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:Literal ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 4 ; + sh:path rdf:predicate ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 13 ; + sh:order 39 ; sh:path biolink:has_attribute ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - 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:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 10 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:OrganismAttribute . - -biolink:PairwiseGeneToGeneInteraction a sh:NodeShape ; - rdfs:subClassOf biolink:GeneToGeneAssociation ; - 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:datatype xsd:string ; - sh:description "interaction relationship type" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 7 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 27 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + 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 24 ; + 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:nodeKind sh:Literal ; - sh:order 31 ; + sh:order 34 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 30 ; - sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "used to 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:Literal ; - sh:order 14 ; + sh:order 17 ; sh:path biolink:original_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:datatype xsd:string ; - sh:description "a human-readable description of an 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:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource 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: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:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ 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:class biolink:MolecularEntity ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; + 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:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 16 ; + 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 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:order 21 ; + sh:path biolink:object_category ] ; + sh:targetClass biolink:ReactionToCatalystAssociation . + +biolink:ReactionToParticipantAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 7 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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 12 ; - sh:path biolink:agent_type ], + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object 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_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:RetrievalSource ; sh:description "A list of 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:order 30 ; sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:integer ; + 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:datatype xsd:string ; + sh:description "An intermediate aggregator resource 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: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:datatype xsd:string ; sh:description "Used to hold 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:Literal ; - sh:order 24 ; + sh:order 27 ; sh:path biolink:object_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:minCount 1 ; sh:order 15 ; - sh:path biolink:original_predicate ], + sh:path biolink:agent_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:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:p_value ], + [ 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:Literal ; + sh:minCount 1 ; sh:order 4 ; - sh:path biolink:qualifier ], + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - 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 "Used to hold the subject 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:subject_label_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:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; + sh:order 32 ; sh:path biolink:adjusted_p_value ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:timepoint ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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_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 "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; + sh:order 6 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "used to 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:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 19 ; + 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 10 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; + sh:order 36 ; sh:path rdf:type ], + [ 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 original relation/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_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 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], + sh:order 24 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; + sh:description "A unique identifier 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: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:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:path biolink: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 biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:subject_category ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 37 ; + sh:path rdfs:label ], + [ sh:description "the side of a reaction being modeled (ie: left or right)" ; + sh:in ( "left" "right" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 2 ; + sh:path biolink:reaction_side ], [ sh:datatype xsd:string ; sh:description "Used to hold 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:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 26 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ] ; - sh:targetClass biolink:PairwiseGeneToGeneInteraction . + sh:description "Used to hold the object label 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:object_label_closure ] ; + sh:targetClass biolink:ReactionToParticipantAssociation . -biolink:Polypeptide a sh:NodeShape ; - rdfs:subClassOf biolink:BiologicalEntity ; +biolink:ReagentTargetedGene 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: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:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path biolink:xref ], + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 14 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - 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:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + 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:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; + sh:order 6 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; + sh:order 9 ; sh:path biolink:category ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], + [ 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 12 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:Polypeptide . + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:targetClass biolink:ReagentTargetedGene . -biolink:PredicateMapping a sh:NodeShape ; +biolink:RegulatoryRegion a sh:NodeShape ; sh:closed true ; - sh:description "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place." ; + sh: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:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:mapped_predicate ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:property [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:species_context_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:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:object_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + 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:nodeKind sh:Literal ; sh:order 3 ; - sh:path biolink:subject_form_or_variant_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:datatype xsd:string ; - 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:path biolink:in_taxon_label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:NamedThing ; - sh:description "a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:narrow_match ], - [ sh:datatype xsd:string ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:subject_context_qualifier ], + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path biolink:object_form_or_variant_qualifier ], - [ sh:datatype xsd:string ; - sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:subject_part_qualifier ], - [ sh:datatype xsd:string ; - 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:Literal ; - sh:order 16 ; - sh:path biolink:anatomical_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_direction_qualifier ], - [ 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 "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:object_direction_qualifier ], + sh:path rdfs:label ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:predicate ], + sh:order 1 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:object_derivative_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path biolink:object_part_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + 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:subject_derivative_qualifier ] ; - sh:targetClass biolink:PredicateMapping . + sh:path biolink:xref ] ; + sh:targetClass biolink:RegulatoryRegion . -biolink:Procedure a sh:NodeShape ; - rdfs:subClassOf biolink:NamedThing ; +biolink:RelationshipQuantifier a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:RelationshipQuantifier . + +biolink:RelationshipType a sh:NodeShape ; sh:closed true ; - sh:description "A series of actions conducted in a certain order or manner" ; + sh:description "An OWL property used as an edge label" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 6 ; - sh:path biolink:category ], + sh:order 0 ; + sh:path biolink:id ] ; + sh:targetClass biolink:RelationshipType . + +biolink:RelativeFrequencyAnalysisResult a sh:NodeShape ; + sh:closed true ; + sh:description "A result of a relative frequency analysis." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path biolink:full_name ], + 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 10 ; + sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - 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:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 10 ; + sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 4 ; + sh:order 8 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - 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 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 11 ; + 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 database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:Procedure . + sh:path biolink:iri ] ; + sh:targetClass biolink:RelativeFrequencyAnalysisResult . -biolink:Protein a sh:NodeShape ; - rdfs:subClassOf biolink:Polypeptide ; +biolink:SensitivityQuantifier a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:SensitivityQuantifier . + +biolink:SequenceAssociation a sh:NodeShape ; sh:closed true ; - sh:description "A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA" ; + sh:description "An association between a sequence feature and a nucleic acid entity it is localized to." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 37 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:description "Used to hold 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:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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 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:datatype xsd:boolean ; + 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:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "Used to hold 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:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ 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:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 6 ; + sh:order 30 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; + [ 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 biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + 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 "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; + sh:order 31 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the 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:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object 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: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:datatype xsd:string ; + sh:description "An intermediate aggregator resource 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 32 ; + sh:path biolink:category ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:order 12 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:Protein . + sh:path biolink:agent_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:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "used to 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:RetrievalSource ; + sh:description "A list of 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:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "used to 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:Publication ; + sh:description "One or more 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:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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:datatype xsd:string ; + sh:description "Used to hold the subject 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:targetClass biolink:SequenceAssociation . -biolink:ReactionToParticipantAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:ChemicalToChemicalAssociation ; +biolink:SequenceFeatureRelationship a sh:NodeShape ; sh:closed true ; + sh:description "For example, a particular exon is part of a particular transcript or gene" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ 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: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:nodeKind sh:Literal ; - 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:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; sh:order 29 ; - sh:path biolink:object_label_closure ], + sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is 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 ], - [ 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:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:p_value ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - 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:order 14 ; + sh:path biolink:original_subject ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:order 4 ; - sh:path rdf:predicate ], + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:timepoint ], + sh:minCount 1 ; + sh:order 30 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an 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:nodeKind sh:Literal ; - sh:order 38 ; - sh:path dct:description ], + sh:order 8 ; + 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:datatype xsd:string ; + sh:description "Used to hold the subject 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:datatype xsd:string ; sh:description "used to 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:Literal ; - sh:order 19 ; + sh:order 16 ; sh:path biolink:original_object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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 15 ; - sh:path biolink:agent_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 9 ; - sh:path biolink:publications ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:deprecated ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical element that is the target of the statement" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh: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 rdf:object ], + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 39 ; + sh:order 36 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 27 ; - 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 "Used to hold the 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:object_category ], - [ sh:class biolink:MolecularEntity ; - sh:description "the chemical entity or entity that is an interactor" ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object 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:datatype xsd:string ; + sh:description "Used to hold the 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:datatype xsd:string ; + sh:description "Used to hold 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 23 ; + 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 3 ; - sh:path rdf:subject ], + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + 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 15 ; + sh:path biolink:original_predicate ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path biolink:knowledge_source ], + sh:path biolink:knowledge_level ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 10 ; + sh:order 7 ; sh:path biolink:has_evidence ], - [ 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:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:category ], - [ sh:description "the side of a reaction being modeled (ie: left or right)" ; - sh:in ( "left" "right" ) ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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: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 biolink:reaction_side ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + 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 32 ; + 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:Literal ; - sh:order 7 ; - sh:path biolink: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 30 ; - sh:path biolink:retrieval_source_ids ], + 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 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_namespace ], + sh:order 24 ; + sh:path biolink:object_namespace ] ; + 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:datatype xsd:string ; + sh:description "Used to hold the subject 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:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ 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:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 33 ; + sh:order 30 ; sh:path biolink:id ], - [ sh:datatype xsd:integer ; - 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:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:stoichiometry ], + sh:order 4 ; + sh:path biolink: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:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; + sh:order 3 ; sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:object_closure ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "used to 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:Literal ; - sh:order 17 ; + sh:order 14 ; 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:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is 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:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:ReactionToParticipantAssociation . - -biolink:SequenceAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - 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:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:SequenceVariant ; + sh:description "variant that modulates the treatment of some disease" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "Used to hold the 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:datatype xsd:string ; + sh:description "used to 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: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:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - 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:class biolink:RetrievalSource ; sh:description "A list of 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:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - 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 17 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - 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 6 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh: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:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_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:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold 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 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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 "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ] ; + 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:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 19 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + 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:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 0 ; + sh:path biolink:iso_abbreviation ], + [ sh:datatype xsd:date ; + 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:datatype xsd:string ; + sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:summary ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 22 ; + 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 21 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:rights ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 7 ; + sh:path biolink:mesh_terms ], + [ sh:datatype xsd:string ; + 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 "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:format ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:license ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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 22 ; - sh:path biolink:object_category_closure ], + sh:order 24 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - 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 21 ; - sh:path biolink:subject_category_closure ], + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:order 9 ; + sh:path dct:type ], + [ sh:datatype xsd:string ; + 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:datatype xsd:string ; + sh:description "Should generally be set to an ontology class defined term for 'serial' or 'journal'." ; + sh:order 20 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + 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:minCount 1 ; - sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:predicate ], + sh:path biolink:volume ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 9 ; - 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:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 36 ; + sh:order 23 ; 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 5 ; - sh:path biolink:qualifiers ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 16 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 2 ; + sh:path biolink:issue ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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 "Serials (journals) should have industry-standard identifier such as from ISSN." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ] ; - sh:targetClass biolink:SequenceAssociation . + sh:minCount 1 ; + sh:order 17 ; + 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 3 ; + sh:path biolink:authors ] ; + sh:targetClass biolink:Serial . -biolink:SocioeconomicAttribute a sh:NodeShape ; - rdfs:subClassOf biolink:Attribute ; +biolink:SeverityValue a sh:NodeShape ; sh:closed true ; - sh:description "Attributes relating to a socioeconomic manifestation" ; + sh:description "describes the severity of a phenotypic feature or disease" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + 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:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + 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 0 ; + sh:path rdfs:label ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:full_name ], [ sh:class biolink:NamedThing ; @@ -30646,12 +24995,10 @@ biolink:SocioeconomicAttribute a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:string ; - 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:Literal ; - 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 10 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -30659,1421 +25006,1055 @@ biolink:SocioeconomicAttribute a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; + [ sh:description "Alternate human-readable names for a thing" ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 14 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:SocioeconomicAttribute . - -biolink:SpecificityQuantifier a sh:NodeShape ; - rdfs:subClassOf biolink:RelationshipQuantifier ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:SpecificityQuantifier . - -biolink:StudyPopulation a sh:NodeShape ; - rdfs:subClassOf biolink:PopulationOfIndividualOrganisms ; - 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:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 6 ; + sh:order 5 ; sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - 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:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ] ; - sh:targetClass biolink:StudyPopulation . - -biolink:TaxonomicRank a sh:NodeShape ; - rdfs:subClassOf biolink:OntologyClass ; - sh:closed true ; - sh:description "A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom)" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 0 ; - sh:path biolink:id ] ; - sh:targetClass biolink:TaxonomicRank . + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ] ; + sh:targetClass biolink:SeverityValue . -biolink:Treatment a sh:NodeShape ; - rdfs:subClassOf biolink:NamedThing ; +biolink:SiRNA a sh:NodeShape ; sh:closed true ; - sh:description "A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures" ; + sh: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:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 8 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:time ; - 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 1 ; + sh:path biolink:xref ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Procedure ; - sh:description "connects an entity to one or more (medical) procedures" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_procedure ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:class biolink:Device ; - sh:description "connects an entity to one or more (medical) devices" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_device ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; + sh:path biolink:in_taxon_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 "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 biolink:category ], + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; + sh:order 13 ; sh:path biolink:deprecated ], - [ sh:class biolink:Drug ; - sh:description "connects an entity to one or more drugs" ; - sh:nodeKind sh:IRI ; + [ sh:description "Alternate human-readable names for a thing" ; sh:order 0 ; - sh:path biolink:has_drug ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:path biolink:synonym ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; + sh:order 5 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 11 ; sh:path dct:description ], - [ 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 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ] ; - sh:targetClass biolink:Treatment . + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier 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:targetClass biolink:SiRNA . -biolink:VariantToDiseaseAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; +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:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - 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:property [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype ; - 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:Literal ; - sh:order 43 ; - sh:path biolink:frequency_qualifier ], + sh:order 5 ; + sh:path biolink:has_chemical_role ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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:deprecated ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:knowledge_source ], + 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 name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "E.g. is pathogenic for" ; + sh:description "" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:path biolink:trade_name ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 15 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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 "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 3 ; + sh:path biolink:max_tolerated_dose ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 12 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:order 0 ; + sh:path biolink:is_metabolite ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], + sh:order 13 ; + 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 11 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:is_toxic ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 30 ; + sh:order 10 ; sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 36 ; + sh:order 16 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ] ; + sh:targetClass biolink:SmallMolecule . + +biolink:Snv a sh:NodeShape ; + sh:closed true ; + sh:description "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], + sh:order 7 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "used to 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:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - 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: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:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 8 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - 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:description "The value in this node property represents the knowledge provider that created or assembled the node 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 "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 4 ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:Gene ; + sh:description "Each allele can be associated with any number of genes" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:object_direction_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 0 ; + sh:path biolink:has_gene ], + [ sh:description "The state of the sequence w.r.t a reference sequence" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:anyURI ; - 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 1 ; + sh:path biolink:has_biological_sequence ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 13 ; + 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 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`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:agent_type ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 10 ; + sh:path biolink:category ] ; + sh:targetClass biolink:Snv . + +biolink:SocioeconomicExposure a sh:NodeShape ; + sh:closed true ; + sh:description "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty)." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:SocioeconomicAttribute ; + sh:description "connects any entity to an attribute" ; + sh:minCount 1 ; + 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 39 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:Disease ; - sh:description "a disease that is associated with that variant" ; + 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:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ 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 rdf:object ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:iri ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated in some way with the disease state" ; + sh:description "A unique 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:datatype xsd:string ; - sh:description "Used to hold 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 6 ; + sh:path biolink:id ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ] ; - sh:targetClass biolink:VariantToDiseaseAssociation . + 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:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ] ; + sh:targetClass biolink:SocioeconomicExposure . -biolink:VariantToGeneAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; +biolink:SocioeconomicOutcome 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:description "An general social or economic outcome, such as healthcare costs, utilization, etc., resulting from an exposure event" ; 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 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:targetClass biolink:SocioeconomicOutcome . + +biolink:SpecificityQuantifier a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:SpecificityQuantifier . + +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 database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to 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 biolink:synonym ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 9 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 11 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - 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 4 ; + sh:path biolink:id ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + 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 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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: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 human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "used to 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 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism 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 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - 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 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 database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; 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:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:path biolink:deprecated ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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 1 ; + sh:path biolink:in_taxon_label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ] ; + sh:targetClass biolink:StudyPopulation . + +biolink:StudyResult a sh:NodeShape ; + sh:closed false ; + sh:description "A collection of data items from a study that are about a particular study subject or experimental unit (the 'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation of this data as evidence." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:order 6 ; + 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 11 ; - sh:path biolink:knowledge_level ], + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - 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:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - 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 15 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:date ; + 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:qualifiers ], + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path rdf:object ], + sh:path biolink:format ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; 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:datatype xsd:string ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the 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:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:description "Alternate human-readable names for a thing" ; sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 36 ; + sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 9 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 30 ; + sh:order 8 ; 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:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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:targetClass biolink:VariantToGeneAssociation . + sh:order 0 ; + sh:path biolink:license ] ; + sh:targetClass biolink:StudyResult . -biolink:Zygosity a sh:NodeShape ; - rdfs:subClassOf biolink:Attribute ; +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:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; + sh:order 9 ; sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - 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 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 5 ; + sh:order 8 ; sh:path biolink:id ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - 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:datatype xsd:date ; + 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:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:provided_by ], + 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:order 14 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - 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:Literal ; sh:order 0 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], + sh:path biolink:license ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; + sh:order 15 ; sh:path biolink:deprecated ], - [ 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:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:order 11 ; + 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:nodeKind sh:Literal ; sh:order 10 ; - sh:path biolink:category ] ; - sh:targetClass biolink:Zygosity . + sh:path biolink:category ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 13 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ] ; + sh:targetClass biolink:StudyVariable . -biolink:AnatomicalEntityToAnatomicalEntityAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; +biolink:SubjectOfInvestigation a sh:NodeShape ; sh:closed false ; + sh:description "An entity that has the role of being studied in an investigation, study, or experiment" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:targetClass biolink:SubjectOfInvestigation . + +biolink:TaxonToTaxonAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource 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:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + 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:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + 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:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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 unique identifier 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:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + 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 22 ; + 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 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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 36 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "used to 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:Literal ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - 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 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:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Used to hold 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:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ 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:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ] ; - sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityAssociation . - -biolink:BiologicalProcessOrActivity a sh:NodeShape ; - rdfs:subClassOf biolink:BiologicalEntity ; - 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:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - 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:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - 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 1 ; - sh:path biolink:has_output ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_input ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:description "Used to hold the 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 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 biolink:enabled_by ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ 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:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + 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:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ] ; - sh:targetClass biolink:BiologicalProcessOrActivity . - -biolink:Case a sh:NodeShape ; - rdfs:subClassOf biolink:IndividualOrganism ; - 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:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - 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:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "An association between individuals of different taxa." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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:order 32 ; + sh:path biolink:category ], [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:description "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 biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:path rdf:subject ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the 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:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:Case . + sh:order 8 ; + sh:path biolink:knowledge_source ] ; + sh:targetClass biolink:TaxonToTaxonAssociation . -biolink:CellLine a sh:NodeShape ; - rdfs:subClassOf biolink:OrganismalEntity ; +biolink:TextMiningResult a sh:NodeShape ; sh:closed true ; + sh:description "A result of text mining." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - 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 13 ; + sh:path dct:description ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; + 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 10 ; + 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 9 ; - sh:path rdf:type ], + sh:path biolink:iri ], + [ sh:datatype xsd:date ; + 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:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 15 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_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:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:id ], [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; + sh:order 4 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:description "Alternate human-readable names for a thing" ; sh:order 7 ; - sh:path biolink:iri ], + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; + 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:targetClass biolink:CellLine . + sh:targetClass biolink:TextMiningResult . -biolink:ChemicalEntityToEntityAssociationMixin a sh:NodeShape ; +biolink:ThingWithTaxon a sh:NodeShape ; sh:closed false ; - sh:description "An interaction between a chemical entity and another entity" ; + sh:description "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" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - 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: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:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; + sh:path biolink:in_taxon_label ] ; + sh:targetClass biolink:ThingWithTaxon . + +biolink:TranscriptToGeneRelationship a sh:NodeShape ; + sh:closed true ; + sh:description "A gene is a collection of transcripts" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource 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:Gene ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity that is an interactor" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ] ; - sh:targetClass biolink:ChemicalEntityToEntityAssociationMixin . - -biolink:ChemicalToChemicalAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - 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:datatype xsd:string ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; sh:description "Used to hold 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:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ 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 "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:boolean ; + 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:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object 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:Publication ; + sh:description "One or more 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 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink: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 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], + sh:order 37 ; + sh:path biolink:deprecated ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ 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:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - 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 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; + sh:order 24 ; + 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:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 34 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "used to 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:Literal ; sh:order 14 ; sh:path biolink:original_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:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier 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:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -32081,851 +26062,644 @@ biolink:ChemicalToChemicalAssociation a sh:NodeShape ; sh:order 18 ; sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], + 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 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: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: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:ChemicalEntity ; - sh:description "the chemical element that is the target of the statement" ; - sh:maxCount 1 ; + sh:path biolink:subject_category ] ; + sh:targetClass biolink:TranscriptToGeneRelationship . + +biolink:TranscriptionFactorBindingSite a sh:NodeShape ; + sh:closed true ; + sh:description "A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that modulates gene transcription" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 rdf:object ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:anyURI ; - 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 "The value in this node property represents the knowledge provider that created or assembled the node 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 "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + 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:datatype xsd:string ; - sh:description "used to 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:nodeKind sh:Literal ; - sh:order 16 ; - 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 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:id ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:description "a 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:qualifiers ], + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 36 ; + sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 14 ; + sh:path biolink:deprecated ] ; + sh:targetClass biolink:TranscriptionFactorBindingSite . + +biolink:VariantAsAModelOfDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 43 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:RetrievalSource ; sh:description "A list of 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:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource 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:datatype xsd:string ; + sh:description "used to 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:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - 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:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is 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:publications ] ; - sh:targetClass biolink:ChemicalToChemicalAssociation . - -biolink:ClinicalEntity a sh:NodeShape ; - rdfs:subClassOf biolink:NamedThing ; - 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:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path biolink:subject_direction_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 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "used to 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:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:SequenceVariant ; + sh:description "A variant that has a role in modeling the disease." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:path rdf:subject ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; + sh:order 34 ; + 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 31 ; sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:ClinicalEntity . - -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:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + 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:nodeKind sh:Literal ; - sh:order 5 ; - sh:path dct:description ], + sh:order 42 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:iri ], + 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 6 ; + sh:order 36 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:id ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold 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:Literal ; - sh:order 4 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 2 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject 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 "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path rdf:type ] ; - sh:targetClass biolink:Entity . - -biolink:EntityToFeatureOrDiseaseQualifiersMixin a sh:NodeShape ; - rdfs:subClassOf biolink:FrequencyQualifierMixin ; - sh:closed false ; - sh:description "Qualifiers for entity to disease or phenotype associations." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:object_aspect_qualifier ], - [ 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 38 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "The relationship to the disease" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path rdf:subject ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:boolean ; + 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:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:predicate ], + sh:order 30 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - 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:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualified_predicate ], + sh:order 40 ; + sh:path biolink:object_aspect_qualifier ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 3 ; + sh:order 41 ; sh:path biolink:object_direction_qualifier ], - [ sh:datatype ; - 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:Literal ; - sh:order 5 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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_direction_qualifier ], - [ 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 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path rdf:object ], + sh:order 35 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ] ; - sh:targetClass biolink:EntityToFeatureOrDiseaseQualifiersMixin . + sh:description "Used to hold the object 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: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:targetClass biolink:VariantAsAModelOfDiseaseAssociation . -biolink:FrequencyQualifierMixin a sh:NodeShape ; - sh:closed false ; - sh:description "Qualifier for frequency type associations" ; +biolink:VariantToDiseaseAssociation a sh:NodeShape ; + sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to 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:Literal ; - sh:order 0 ; - sh:path biolink:frequency_qualifier ], - [ 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 14 ; + 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 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:description "E.g. is pathogenic for" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; sh:order 1 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - 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:Literal ; - sh:order 2 ; sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path biolink:subject_direction_qualifier ], + [ 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 3 ; - sh:path rdf:object ] ; - sh:targetClass biolink:FrequencyQualifierMixin . - -biolink:GeneProductMixin a sh:NodeShape ; - rdfs:subClassOf biolink:GeneOrGeneProduct ; - 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:datatype xsd:string ; - 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:nodeKind sh:Literal ; sh:order 2 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:GeneProductMixin . - -biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - 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 24 ; - 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:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the phenotypic feature" ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - 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 9 ; - sh:path biolink:publications ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 1 ; + sh:order 41 ; sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 27 ; - 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 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 39 ; + sh:order 36 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold 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:Literal ; - sh:order 26 ; + 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 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 33 ; + sh:order 30 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 38 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - 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:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the subject 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 "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:datatype xsd:string ; + sh:description "Used to hold 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:Literal ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource 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:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; + sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 17 ; - sh:path biolink:original_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:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:qualified_predicate ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - 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 "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; + sh:order 3 ; sh:path biolink:negated ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ 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:Literal ; - sh:order 40 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "used to 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 43 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_object ], + sh:order 31 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; - sh:path biolink:object_category ], + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:double ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_quotient ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 40 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 10 ; + sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], + sh:order 17 ; + 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 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - 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 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + 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 42 ; + sh:path biolink:qualified_predicate ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path rdfs:label ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; + sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_count ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink: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 8 ; - sh:path biolink:qualifiers ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "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 35 ; + 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:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:path rdf:subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "used to 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:Literal ; sh:order 16 ; - sh:path biolink:timepoint ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_total ] ; - sh:targetClass biolink:GeneToDiseaseOrPhenotypicFeatureAssociation . + sh:description "Used to hold the 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:targetClass biolink:VariantToDiseaseAssociation . -biolink:NoncodingRNAProduct a sh:NodeShape ; - rdfs:subClassOf biolink:RNAProduct ; - sh:closed true ; +biolink:VariantToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ 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:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - 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:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ 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:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + 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:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - 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:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated with some other entity" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; + sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ] ; - sh:targetClass biolink:NoncodingRNAProduct . + sh:path rdf:subject ] ; + sh:targetClass biolink:VariantToEntityAssociationMixin . -biolink:OrganismTaxonToOrganismTaxonAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - sh:closed false ; - sh:description "A relationship between two organism taxon nodes" ; +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:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to 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:RetrievalSource ; + sh:description "A list of 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 36 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + 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:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], + sh:order 31 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OrganismTaxon ; - sh:description "organism taxon that is the subject of the association" ; + sh:description "An intermediate aggregator resource 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 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 0 ; - sh:path rdf:subject ], + 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 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ 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:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the 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:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], + sh:order 37 ; + sh:path biolink:deprecated ], [ sh:defaultValue "not_provided" ; sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; @@ -32933,2794 +26707,2823 @@ biolink:OrganismTaxonToOrganismTaxonAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 34 ; + sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 35 ; + sh:path dct:description ], + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated with some other entity" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:Gene ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "Used to hold 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:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + 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 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - 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 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to 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 "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 4 ; + sh:path biolink: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: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:datatype xsd:string ; - 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:nodeKind sh:Literal ; - 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:order 30 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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:datatype xsd:string ; + sh:description "used to 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 point in time" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path biolink:p_value ], + [ 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 36 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold 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:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is 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:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 33 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is 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: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: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:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to 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:original_object ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], [ sh:defaultValue "not_provided" ; sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; + sh:order 15 ; sh:path biolink:knowledge_level ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:qualifier ], + [ 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:datatype xsd:string ; sh:description "used to 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:Literal ; - sh:order 14 ; + sh:order 18 ; sh:path biolink:original_subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:OntologyClass ; + sh:description "Optional quantitative value indicating degree of expression." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 0 ; + sh:path biolink:quantifier_qualifier ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; + sh:minCount 1 ; sh:order 34 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:OrganismTaxonToOrganismTaxonAssociation . - -biolink:Outcome a sh:NodeShape ; - sh:closed false ; - sh:description "An entity that has the role of being the consequence of an exposure event. This is an abstract mixin grouping of various categories of possible biological or non-biological (e.g. clinical) outcomes." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:Outcome . - -biolink:PhysicalEssenceOrOccurrent a sh:NodeShape ; - sh:closed false ; - sh:description "Either a physical or processual entity." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:PhysicalEssenceOrOccurrent . - -biolink:RNAProduct a sh:NodeShape ; - rdfs:subClassOf biolink:Transcript ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; sh:order 13 ; - sh:path biolink:deprecated ], + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object 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:object_label_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 40 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - 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:class biolink:LifeStage ; + sh:description "stage during which gene or protein expression of takes place." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:path biolink:stage_qualifier ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], + sh:order 17 ; + 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:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object 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_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:class biolink:OntologyClass ; + sh:description "Used to hold the 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 26 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated with some other entity" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path rdf:subject ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:order 7 ; + 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 dct:description ], + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:RNAProduct . - -biolink:RegulatoryRegion a sh:NodeShape ; - rdfs:subClassOf biolink:BiologicalEntity ; - 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:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 28 ; + 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 36 ; + 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 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:retrieval_source_ids ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:p_value ], + [ 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:Literal ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:order 5 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject 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_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:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 19 ; + sh:path biolink:original_predicate ], + [ 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:nodeKind sh:Literal ; - sh:order 8 ; - 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:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], + sh:order 6 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_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 29 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; + sh:order 41 ; sh:path biolink:deprecated ], + [ 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:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; + sh:description "Used to hold 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:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 27 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 37 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 39 ; + 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:Literal ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - 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 22 ; + 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:minCount 1 ; - sh:nodeKind sh:Literal ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_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:id ] ; - sh:targetClass biolink:RegulatoryRegion . + sh:path biolink:expression_site ] ; + sh:targetClass biolink:VariantToGeneExpressionAssociation . -biolink:Drug a sh:NodeShape ; - rdfs:subClassOf biolink:MolecularMixture ; +biolink:VariantToPhenotypicFeatureAssociation 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:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; - 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 2 ; - sh:path biolink:highest_FDA_approval_status ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "Used to hold 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:Literal ; - sh:order 20 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:xref ], + sh:order 24 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - 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 "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - 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 43 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:drug_regulatory_status_world_wide ], + sh:order 39 ; + sh:path biolink:has_count ], [ sh:datatype xsd:string ; - sh: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: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:Literal ; - sh:order 1 ; - sh:path biolink:is_supplement ], - [ 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:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 6 ; - sh:path biolink:available_from ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 3 ; + sh:path biolink:sex_qualifier ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:minCount 1 ; sh:order 12 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + 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:Literal ; - sh:order 17 ; - 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:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 15 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ 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:is_toxic ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + 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:nodeKind sh:Literal ; - sh:order 18 ; - sh:path dct:description ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 4 ; - sh:path biolink:routes_of_delivery ], - [ sh:datatype xsd:string ; - sh:description "" ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:trade_name ] ; - sh:targetClass biolink:Drug . - -biolink:ExposureEvent a sh:NodeShape ; - rdfs:subClassOf biolink:OntologyClass ; - sh:closed false ; - sh:description "A (possibly time bounded) incidence of a feature of the environment of an organism that influences one or more phenotypic features of that organism, potentially mediated by genes" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 40 ; + sh:path biolink:has_total ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + 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:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 48 ; + 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:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:id ] ; - sh:targetClass biolink:ExposureEvent . - -biolink:GeneToGeneAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - 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:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 5 ; + sh:path biolink: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:order 23 ; sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "used to 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:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 21 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is 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:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:path biolink:subject_category ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path biolink:has_quotient ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 44 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 34 ; + 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 7 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; + sh:order 27 ; sh:path biolink:object_label_closure ], + [ 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 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:datatype xsd:boolean ; + 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:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated in some way with the phenotype state" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:id ], - [ 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:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + 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 33 ; + sh:path biolink:category ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:object_direction_qualifier ], + [ 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:BlankNodeOrIRI ; + sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:order 45 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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:datatype xsd:string ; + 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 47 ; + sh:path biolink:qualified_predicate ], + [ sh:defaultValue "not_provided" ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; + sh:order 29 ; sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - 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 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:has_percentage ] ; + 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:defaultValue "not_provided" ; + sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the 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:object_namespace ], + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 31 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:integer ; + sh:description "number in object population that carry a particular allele, aka allele count" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], - [ 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:order 3 ; + sh:path biolink:has_count ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 41 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 42 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 38 ; + sh:path rdf:type ], + [ sh:datatype xsd:double ; + 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:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Publication ; - sh:description "One or more 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 5 ; + 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 20 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 15 ; + 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 object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 27 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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:knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], + sh:order 8 ; + sh:path biolink:negated ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 40 ; + 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 36 ; + sh:path biolink:iri ], + [ sh:description "a point in time" ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; + sh:order 30 ; 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:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; sh:order 32 ; - sh:path biolink:category ], + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 14 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:integer ; + sh:description "number all populations that carry a particular allele, aka allele number" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:order 4 ; + sh:path biolink:has_total ], [ sh:datatype xsd:string ; - sh:description "used to 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:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; + sh:order 35 ; + sh:path biolink:id ], + [ 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 17 ; - sh:path biolink:subject_category ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "Used to hold 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:Literal ; - sh:order 23 ; + sh:order 28 ; sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 33 ; + sh:path biolink:p_value ], [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:agent_type ], + [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; sh:order 11 ; - sh:path biolink:knowledge_level ], + 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 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:order 34 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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 29 ; + sh:path biolink:object_namespace ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 39 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:path biolink:qualifier ], + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "the population that is observed to have the frequency" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + 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 10 ; + 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 37 ; + sh:path biolink:category ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:has_percentage ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the 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:order 26 ; sh:path biolink:subject_category_closure ], - [ 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 7 ; - sh:path biolink:has_evidence ], + sh:order 22 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to 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:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ] ; - sh:targetClass biolink:GeneToGeneAssociation . + sh:order 21 ; + sh:path biolink:original_object ] ; + sh:targetClass biolink:VariantToPopulationAssociation . -biolink:IndividualOrganism a sh:NodeShape ; - rdfs:subClassOf biolink:OrganismalEntity ; +biolink:Vertebrate 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:description "A sub-phylum of animals consisting of those having a bony or cartilaginous vertebral column." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_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:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 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. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; sh:order 8 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:IndividualOrganism . - -biolink:MaterialSample a sh:NodeShape ; - rdfs:subClassOf biolink:PhysicalEntity ; - 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:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; + sh:order 10 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ 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:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; + sh:order 13 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; + sh:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:description "Alternate human-readable names for a thing" ; sh:order 5 ; + 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:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; - sh:order 10 ; + sh:order 12 ; sh:path biolink:has_attribute ] ; - sh:targetClass biolink:MaterialSample . + sh:targetClass biolink:Vertebrate . -biolink:Pathway a sh:NodeShape ; - rdfs:subClassOf biolink:BiologicalProcess ; +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:datatype xsd:string ; - sh:description "a long-form human readable name 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 3 ; + sh:path biolink:xref ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; + sh:order 4 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:Attribute ; + sh:description "may often be an organism 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 8 ; + sh:path biolink:category ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 10 ; sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 0 ; + sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh: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:order 0 ; sh:path biolink:in_taxon ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], - [ sh: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:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + [ sh:description "Alternate human-readable names for a thing" ; sh:order 5 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; + 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 15 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ 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:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ] ; - sh:targetClass biolink:Pathway . + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_label ] ; + sh:targetClass biolink:Virus . -biolink:PlanetaryEntity a sh:NodeShape ; - rdfs:subClassOf biolink:NamedThing ; +biolink:WebPage a sh:NodeShape ; sh:closed true ; - sh:description "Any entity or process that exists at the level of the whole planet" ; + 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:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 10 ; + sh:path biolink:creation_date ], + [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; + sh:order 18 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:order 6 ; + sh:path dct:type ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:format ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 13 ; sh:path biolink:synonym ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 19 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 6 ; - sh:path biolink:category ], + sh:description "keywords tagging a publication" ; + sh:order 3 ; + sh:path biolink:keywords ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; + sh:order 21 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; + sh:maxCount 1 ; sh:order 7 ; - sh:path rdf:type ], + sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + 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:nodeKind sh:Literal ; - sh:order 2 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:id ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 12 ; sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ] ; - sh:targetClass biolink:PlanetaryEntity . - -biolink:RelationshipQuantifier a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:RelationshipQuantifier . - -biolink:SequenceFeatureRelationship a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; - sh:closed true ; - sh:description "For example, a particular exon is part of a particular transcript or gene" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink: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:order 15 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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: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 2 ; - sh:path rdf:object ], + sh:order 0 ; + sh:path biolink:authors ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; + sh:order 17 ; sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_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 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh: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 "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 1 ; + sh:path biolink:pages ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 4 ; + sh:path biolink:mesh_terms ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:deprecated ], + sh:order 16 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:anyURI ; - 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 "executive summary of a publication" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 2 ; + sh:path biolink:summary ] ; + sh:targetClass biolink:WebPage . + +biolink:Behavior 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:nodeKind sh:Literal ; - sh:order 35 ; - 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 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 13 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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 unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:id ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 14 ; + sh:path dct:description ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:path biolink:xref ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:in_taxon_label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - 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:order 2 ; + 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 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], + sh:order 3 ; + sh:path biolink:enabled_by ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - 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:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "used to 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 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; 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:path biolink:deprecated ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 15 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 12 ; + sh:path rdf:type ] ; + sh:targetClass biolink:Behavior . + +biolink:BehavioralFeature a sh:NodeShape ; + sh:closed true ; + sh:description "A phenotypic feature which is behavioral in nature." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; + sh:order 7 ; sh:path biolink:iri ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 36 ; + sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:predicate ], + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + 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:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink: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:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "used to 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 value in this node property represents the knowledge provider that created or assembled the node 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:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + 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:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the 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 13 ; + sh:path biolink:deprecated ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ] ; - sh:targetClass biolink:SequenceFeatureRelationship . + sh:order 11 ; + sh:path dct:description ] ; + sh:targetClass biolink:BehavioralFeature . -biolink:Transcript a sh:NodeShape ; - rdfs:subClassOf biolink:BiologicalEntity ; +biolink:CellularComponent a sh:NodeShape ; sh:closed true ; - sh:description "An RNA synthesized on a DNA or RNA template by an RNA polymerase." ; + sh:description "A location in or around a cell" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:class biolink:Attribute ; + sh:description "may often be an organism 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:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], [ sh:datatype xsd:string ; - 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: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. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; + [ sh:description "Alternate human-readable names for a thing" ; sh:order 5 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + 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 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 biolink:in_taxon_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:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:CellularComponent . + +biolink:ClinicalAttribute a sh:NodeShape ; + sh:closed true ; + sh:description "Attributes relating to a clinical manifestation" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:order 11 ; sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:description "a human-readable 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 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; + sh:order 10 ; sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - 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:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh: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:Literal ; + 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:iri ], + sh:path biolink:xref ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 13 ; 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:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ] ; - sh:targetClass biolink:Transcript . - -biolink:ChemicalMixture a sh:NodeShape ; - rdfs:subClassOf biolink:ChemicalEntity ; - 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 "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], + sh:order 4 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 13 ; + sh:order 5 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; + [ 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:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:deprecated ] ; + 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:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 9 ; + sh:order 4 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; + sh:order 12 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:trade_name ], + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; + sh:order 15 ; sh:path biolink:deprecated ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - 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 8 ; - sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 6 ; + 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:nodeKind sh:Literal ; - sh:order 15 ; + sh:order 10 ; sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:date ; + 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:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path biolink:is_supplement ], - [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:path biolink:license ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:is_toxic ], + sh:order 9 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:synonym ], + sh:minCount 1 ; + sh:order 8 ; + 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:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 19 ; + sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - 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 2 ; - 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, 'clinical approval status.'" ; - 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 1 ; - sh:path biolink:highest_FDA_approval_status ] ; - sh:targetClass biolink:ChemicalMixture . + sh:path biolink:format ] ; + sh:targetClass biolink:Dataset . -biolink:ClinicalAttribute a sh:NodeShape ; - rdfs:subClassOf biolink:Attribute ; +biolink:DatasetDistribution a sh:NodeShape ; sh:closed true ; - sh:description "Attributes relating to a clinical manifestation" ; + sh:description "an item that holds distribution level information about a dataset." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 5 ; + sh:order 9 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 8 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; + sh:order 1 ; + sh:path biolink:license ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 14 ; sh:path dct:description ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; + [ sh:datatype xsd:string ; + sh:maxCount 1 ; sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 10 ; - sh:path biolink:category ], + sh:path biolink:rights ], + [ 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:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:distribution_download_url ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:description "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 7 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:iri ], + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:format ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; + sh:order 16 ; sh:path biolink:deprecated ], - [ 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:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 6 ; sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:ClinicalAttribute . + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:targetClass biolink:DatasetDistribution . -biolink:FunctionalAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:Association ; +biolink:Device 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: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:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + 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 human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 11 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 5 ; + sh:path biolink:iri ], + [ 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:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "class describing the activity, process or localization of the gene product" ; + sh:path biolink:has_attribute ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:path biolink: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 6 ; + sh:path biolink:category ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 9 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 7 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 30 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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 4 ; + sh:path biolink:id ] ; + 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 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 "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + 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:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdfs:label ], + sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 36 ; + sh:order 12 ; 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 6 ; - sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; + sh:order 7 ; 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:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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:order 10 ; + sh:path rdfs:label ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - 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:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ] ; + 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: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 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 1 ; + sh:path 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 "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:category ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 2 ; + sh:path biolink:in_taxon_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 human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; + sh:order 14 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - 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: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:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ], + [ sh:datatype xsd:string ; + sh:order 10 ; + 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 "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:agent_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:order 9 ; + sh:path biolink:category ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 6 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 3 ; + sh:path biolink:provided_by ] ; + sh:targetClass biolink: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 "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ] ; - sh:targetClass biolink:FunctionalAssociation . + sh:order 2 ; + sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:synonym ] ; + sh:targetClass biolink:GeneProductMixin . -biolink:LifeStage a sh:NodeShape ; - rdfs:subClassOf biolink:OrganismalEntity ; +biolink:GeneticInheritance a sh:NodeShape ; sh:closed true ; - sh:description "A stage of development or growth of an organism, including post-natal adult stages" ; + 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:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; + sh:property [ sh:description "Alternate human-readable names for a thing" ; sh:order 5 ; sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; + 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:datatype xsd:string ; - 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 10 ; + sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; 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 1 ; + sh:path biolink:in_taxon_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:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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: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:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:LifeStage . + sh:path biolink:in_taxon ] ; + sh:targetClass biolink:GeneticInheritance . -biolink:NucleicAcidEntity a sh:NodeShape ; - rdfs:subClassOf biolink:MolecularEntity ; - 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." ; +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:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:max_tolerated_dose ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:path biolink:license ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; + sh:order 12 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:trade_name ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], + sh:order 9 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:is_toxic ], + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:is_metabolite ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 15 ; - sh:path biolink:category ], + sh:order 2 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:iri ], + 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 19 ; + sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdf:type ], + [ sh:datatype xsd:date ; + 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:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; + sh:order 4 ; 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 9 ; - sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; + sh:order 13 ; sh:path dct:description ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 6 ; - sh:path biolink:available_from ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:deprecated ], - [ 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:targetClass biolink:NucleicAcidEntity . + 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:targetClass biolink:InformationContentEntity . -biolink:CellularOrganism a sh:NodeShape ; - rdfs:subClassOf biolink:OrganismalEntity ; +biolink:Onset a sh:NodeShape ; sh:closed true ; - sh:description "" ; + sh:description "The age group in which (disease) symptom manifestations appear." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 4 ; + sh:order 8 ; 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:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ 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:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; + 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: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. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 14 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 6 ; - sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; + sh:order 11 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ] ; + sh:targetClass biolink:Onset . + +biolink:OrganismalEntity a sh:NodeShape ; + sh:closed false ; + sh:description "A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + 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 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:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the 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 2 ; + sh:path biolink:provided_by ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:in_taxon_label ] ; - sh:targetClass biolink:CellularOrganism . + sh:path biolink:in_taxon_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:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ 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:datatype xsd:string ; + sh:description "A unique identifier 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 8 ; + sh:path biolink:category ] ; + sh:targetClass biolink:OrganismalEntity . -biolink:GeneToDiseaseAssociation a sh:NodeShape ; - rdfs:subClassOf biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; +biolink:PredicateMapping a sh:NodeShape ; sh:closed true ; + sh:description "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:anyURI ; - 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:datatype xsd:string ; + sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - 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 10 ; - sh:path biolink:has_evidence ], + sh:order 4 ; + sh:path biolink:subject_part_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to 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 qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - 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:order 13 ; + sh:path biolink:object_derivative_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:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 15 ; + sh:path biolink:causal_mechanism_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 2 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + 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:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:negated ], + sh:order 0 ; + sh:path biolink:mapped_predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:double ; + sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 11 ; + sh:path biolink:object_form_or_variant_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:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 1 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], + sh:order 3 ; + sh:path biolink:subject_form_or_variant_qualifier ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed 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 "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:knowledge_source ], + sh:order 12 ; + sh:path biolink:object_part_qualifier ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + 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:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdfs:label ], + sh:order 8 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:subject_derivative_qualifier ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; + sh:order 9 ; sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + [ sh:datatype xsd:string ; + 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:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:species_context_qualifier ], + [ sh: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 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:order 20 ; + sh:path biolink:broad_match ], + [ 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 24 ; - sh:path biolink:subject_category_closure ], + sh:order 19 ; + sh:path biolink:narrow_match ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - 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 9 ; - sh:path biolink:publications ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:p_value ], + sh:order 6 ; + sh:path biolink:subject_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ 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:order 14 ; + sh:path biolink:object_context_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:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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:Literal ; - sh:order 27 ; - sh:path biolink:object_namespace ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], + sh:order 2 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - 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 25 ; - sh:path biolink:object_category_closure ], + sh:order 7 ; + 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 6 ; + sh:path biolink:category ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:datatype xsd:string ; - sh:description "Used to hold 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 value in this node property represents the knowledge provider that created or assembled the node 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:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_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:order 9 ; + sh:path dct:description ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 5 ; - sh:path biolink:sex_qualifier ], + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:Procedure . + +biolink:SocioeconomicAttribute a sh:NodeShape ; + sh:closed true ; + sh:description "Attributes relating to a socioeconomic manifestation" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "used to 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:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + 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 10 ; + sh:path biolink:category ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:order 12 ; + sh:path dct:description ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:qualified_predicate ], - [ 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:nodeKind sh:IRI ; + sh:order 3 ; + 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 7 ; + sh:path biolink:xref ], + [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh: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:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "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 14 ; + sh:path biolink:deprecated ], + [ 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:subject_aspect_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 4 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:SocioeconomicAttribute . + +biolink:TaxonomicRank a sh:NodeShape ; + sh:closed true ; + sh:description "A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom)" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:id ] ; + sh:targetClass biolink:TaxonomicRank . + +biolink:Treatment a sh:NodeShape ; + sh:closed true ; + sh:description "A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Drug ; + sh:description "connects an entity to one or more drugs" ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:order 0 ; + sh:path biolink:has_drug ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_total ], + sh:order 13 ; + sh:path dct:description ], + [ sh:class biolink:Device ; + sh:description "connects an entity to one or more (medical) devices" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_device ], [ sh:datatype xsd:string ; - sh: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 "The value in this node property represents the knowledge provider that created or assembled the node 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:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:id ], + sh:order 10 ; + 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 9 ; + sh:path biolink:iri ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 36 ; + sh:order 11 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path dct:description ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + 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 5 ; + sh:path biolink:xref ], + [ sh:class biolink:Procedure ; + sh:description "connects an entity to one or more (medical) procedures" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_procedure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - 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 15 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:subject_closure ], + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ] ; - sh:targetClass biolink:GeneToDiseaseAssociation . + sh:order 3 ; + sh:path biolink:timepoint ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:full_name ] ; + sh:targetClass biolink:Treatment . -biolink:MolecularActivity a sh:NodeShape ; - rdfs:subClassOf biolink:BiologicalProcessOrActivity ; +biolink:Zygosity 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:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; + sh:property [ sh:description "Alternate human-readable names for a thing" ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 11 ; - 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 4 ; + 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: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:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; + sh:order 14 ; sh:path biolink:deprecated ], - [ 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:datatype xsd:string ; - sh:nodeKind sh:Literal ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:order 12 ; - 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:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path rdfs:label ], + 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: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:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:in_taxon_label ], - [ 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:class biolink:MacromolecularMachineMixin ; - sh:description "The gene product, gene, or complex that catalyzes the reaction" ; - sh:nodeKind sh:BlankNodeOrIRI ; - 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 15 ; - sh:path biolink:has_attribute ], + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ] ; - sh:targetClass biolink:MolecularActivity . + sh:order 11 ; + sh:path rdf:type ] ; + sh:targetClass biolink:Zygosity . -biolink:PopulationOfIndividualOrganisms a sh:NodeShape ; - rdfs:subClassOf biolink:OrganismalEntity ; +biolink:Case 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:description "An individual (human) organism that has a patient role in some clinical context." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; - sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 11 ; + sh:path dct:description ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 1 ; + sh:path biolink:in_taxon_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:datatype xsd:string ; sh:description "A unique 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:Literal ; 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 3 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + 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 0 ; - sh:path biolink:in_taxon ], + sh:path biolink:in_taxon ] ; + sh:targetClass biolink:Case . + +biolink:CellLine 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 7 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier 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 8 ; + sh:path biolink:category ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - 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 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 0 ; + sh:path biolink:in_taxon ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:PopulationOfIndividualOrganisms . + 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 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ] ; + sh:targetClass biolink:CellLine . -biolink:StudyResult a sh:NodeShape ; - rdfs:subClassOf biolink:InformationContentEntity ; - 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." ; +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:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 3 ; - sh:path biolink:creation_date ], + 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 "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:rights ], + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; + sh:order 13 ; sh:path biolink:deprecated ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; - sh:order 14 ; + sh:order 12 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 6 ; + sh:path biolink:id ] ; + sh:targetClass biolink:IndividualOrganism . + +biolink:Outcome a sh:NodeShape ; + sh:closed false ; + sh:description "An entity that has the role of being the consequence of an exposure event. This is an abstract mixin grouping of various categories of possible biological or non-biological (e.g. clinical) outcomes." ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:Outcome . + +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:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; + 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 database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 8 ; + sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 5 ; + sh:path biolink:synonym ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:StudyResult . + sh:order 10 ; + 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 "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:targetClass biolink:Transcript . biolink:BiologicalProcess a sh:NodeShape ; - rdfs:subClassOf biolink:BiologicalProcessOrActivity ; sh:closed true ; sh:description "One or more causally connected executions of molecular functions" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], + sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - 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 6 ; + sh:path biolink:provided_by ], [ 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:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:in_taxon_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 database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ 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:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 5 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; sh:order 12 ; 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 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; sh:order 0 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 13 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 14 ; sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ] ; + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ] ; sh:targetClass biolink:BiologicalProcess . -biolink:ChemicalEntityOrGeneOrGeneProduct a sh:NodeShape ; - sh:closed false ; - sh:description "A union of chemical entities and children, and gene or gene product. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities." ; +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:targetClass biolink:ChemicalEntityOrGeneOrGeneProduct . + sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 17 ; + 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 15 ; + sh:path biolink:category ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "" ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:trade_name ], + [ sh:datatype xsd:string ; + 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 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 11 ; + 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:datatype xsd:string ; + sh:description "" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:is_supplement ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier 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:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:deprecated ], + [ 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 "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, 'clinical approval status.'" ; + 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 2 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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: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:datatype xsd:string ; + sh:order 16 ; + sh:path rdf:type ], + [ 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 "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 6 ; + sh:path biolink:available_from ], + [ sh:datatype xsd:boolean ; + 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 "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + 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 3 ; + sh:path biolink:drug_regulatory_status_world_wide ] ; + sh:targetClass biolink:Drug . -biolink:MacromolecularMachineMixin a sh:NodeShape ; +biolink:ExposureEvent a sh:NodeShape ; sh:closed false ; - sh:description "A union of gene locus, gene product, and macromolecular complex. These are the basic units of function in a cell. They either carry out individual biological activities, or they encode molecules which do this." ; + sh:description "A (possibly time bounded) incidence of a feature of the environment of an organism that influences one or more phenotypic features of that organism, potentially mediated by genes" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:description "A unique identifier 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 point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:MacromolecularMachineMixin . + sh:path biolink:timepoint ] ; + sh:targetClass biolink:ExposureEvent . -biolink:PhysicalEntity a sh:NodeShape ; - rdfs:subClassOf biolink:NamedThing ; +biolink:MaterialSample a sh:NodeShape ; sh:closed true ; - sh:description "An entity that has material reality (a.k.a. physical essence)." ; + 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:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 9 ; + 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:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:datatype xsd:string ; + sh:description "A unique identifier 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 "Alternate human-readable names for a thing" ; sh:order 3 ; sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; sh:order 6 ; sh:path biolink:category ], [ sh:class biolink:Attribute ; @@ -35728,1221 +29531,918 @@ biolink:PhysicalEntity a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path rdfs:label ], + sh:path rdfs:label ] ; + sh:targetClass biolink:MaterialSample . + +biolink:Pathway a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; + sh:order 6 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ 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 long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:deprecated ], + [ 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: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:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:iri ], + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 4 ; + sh:order 0 ; sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ] ; - sh:targetClass biolink:PhysicalEntity . - -biolink:Genotype a sh:NodeShape ; - rdfs:subClassOf biolink:BiologicalEntity ; - 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: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 13 ; + 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 11 ; + sh:path biolink:category ], + [ 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:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:path biolink:enabled_by ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 14 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 7 ; - sh:path biolink:full_name ], - [ sh:class biolink:Zygosity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_zygosity ], + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 14 ; + sh:order 15 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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: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: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:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 10 ; + sh:order 8 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:synonym ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; + sh:order 13 ; sh:path biolink:deprecated ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 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 0 ; + sh:path biolink:in_taxon ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism 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 long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:in_taxon_label ], + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its 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 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:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:has_biological_sequence ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:xref ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 2 ; + sh:order 6 ; sh:path biolink:id ] ; - sh:targetClass biolink:Genotype . + sh:targetClass biolink:LifeStage . -biolink:MolecularEntity a sh:NodeShape ; - rdfs:subClassOf biolink:ChemicalEntity ; +biolink:NucleicAcidEntity a sh:NodeShape ; sh:closed true ; - sh:description "A molecular entity is a chemical entity composed of individual or covalently bonded atoms." ; + 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:datatype xsd:string ; + sh:property [ 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:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 10 ; + sh:order 3 ; sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:is_toxic ], + [ sh:datatype xsd:string ; + sh:order 16 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; + sh:order 7 ; sh:path biolink:max_tolerated_dose ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 12 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ 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: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:nodeKind sh:Literal ; sh:order 17 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:path rdfs:label ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 2 ; + sh:path biolink:in_taxon_label ], [ 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:order 9 ; sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdfs:label ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 11 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; + sh:order 5 ; sh:path biolink:trade_name ], - [ sh:datatype xsd:boolean ; - sh:description "indicates whether a molecular entity is a metabolite" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:is_metabolite ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 2 ; - sh:path biolink:available_from ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:iri ], [ 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:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:MolecularEntity . - -biolink:OrganismalEntity a sh:NodeShape ; - rdfs:subClassOf biolink:BiologicalEntity ; - 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:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - 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 12 ; + sh:order 19 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; + sh:order 15 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 20 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 "Alternate human-readable names for a thing" ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; + sh:order 12 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:boolean ; + sh:description "" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 8 ; + sh:path biolink:is_toxic ], + [ sh:datatype xsd:boolean ; + sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - 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 0 ; - sh:path biolink:in_taxon ] ; - sh:targetClass biolink:OrganismalEntity . + sh:order 1 ; + sh:path biolink:in_taxon ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 6 ; + sh:path biolink:available_from ] ; + sh:targetClass biolink:NucleicAcidEntity . -biolink:SequenceVariant a sh:NodeShape ; - rdfs:subClassOf biolink:BiologicalEntity ; +biolink:MolecularActivity 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:description "An execution of a molecular function carried out by a gene product or macromolecular complex." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], - [ 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 3 ; + sh:order 4 ; sh:path biolink:in_taxon ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; + sh:order 12 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path dct:description ], + 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:class biolink:MacromolecularMachineMixin ; + sh:description "The gene product, gene, or complex that catalyzes the reaction" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 2 ; + 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 biolink:in_taxon_label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; + sh:order 16 ; sh:path biolink:deprecated ], - [ sh:class biolink:Gene ; - sh:description "Each allele can be associated with any number of genes" ; + [ sh:class biolink:MolecularEntity ; + sh:description "A chemical entity that is the output for the reaction" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 2 ; + sh:path biolink:has_output ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 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. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 10 ; + sh:order 11 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 8 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 14 ; + sh:path dct:description ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:MolecularEntity ; + sh:description "A chemical entity that is the input for the reaction" ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The state of the sequence w.r.t a reference sequence" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:has_biological_sequence ] ; - sh:targetClass biolink:SequenceVariant . + sh:path biolink:has_input ] ; + sh:targetClass biolink:MolecularActivity . -biolink:Agent a sh:NodeShape ; - rdfs:subClassOf biolink:AdministrativeEntity ; +biolink:PopulationOfIndividualOrganisms 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: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:datatype xsd:string ; - 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:minCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_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:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], + [ 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:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 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:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path rdf:type ], + sh:path rdf:type ] ; + sh:targetClass biolink:PopulationOfIndividualOrganisms . + +biolink:MacromolecularMachineMixin a sh:NodeShape ; + sh:closed false ; + sh:description "A union of gene locus, gene product, and macromolecular complex. These are the basic units of function in a cell. They either carry out individual biological activities, or they encode molecules which do this." ; + 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 0 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:MacromolecularMachineMixin . + +biolink:MolecularEntity a sh:NodeShape ; + sh:closed true ; + sh:description "A molecular entity is a chemical entity composed of individual or covalently bonded atoms." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 16 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 14 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:is_metabolite ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 2 ; + 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:path biolink:xref ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "" ; + sh:maxCount 1 ; + sh:order 1 ; + 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 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 12 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - 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:description "A unique 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:Literal ; - sh:order 6 ; + sh:order 10 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:max_tolerated_dose ], + [ sh:datatype xsd:string ; + sh:order 13 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; + sh:order 6 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?)." ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:address ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - 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:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:affiliation ] ; - sh:targetClass biolink:Agent . + sh:order 15 ; + 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 5 ; + sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:boolean ; + sh:description "" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:is_toxic ] ; + sh:targetClass biolink:MolecularEntity . -biolink:ChemicalRole a sh:NodeShape ; - rdfs:subClassOf biolink:Attribute ; +biolink:PhysicalEntity 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: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:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; + sh:description "An entity that has material reality (a.k.a. physical essence)." ; + 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:order 10 ; 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:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 5 ; + sh:order 4 ; sh:path biolink:id ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - 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:Literal ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; + sh:path biolink:provided_by ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 1 ; - sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; + sh:order 5 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - 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 1 ; + sh:path biolink:xref ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; + sh:order 9 ; sh:path dct:description ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ] ; - sh:targetClass biolink:ChemicalRole . + sh:order 11 ; + sh:path biolink:deprecated ] ; + sh:targetClass biolink:PhysicalEntity . -biolink:InformationContentEntity a sh:NodeShape ; - rdfs:subClassOf biolink:NamedThing ; +biolink:ChemicalEntityOrGeneOrGeneProduct 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:description "A union of chemical entities and children, and gene or gene product. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; + sh:targetClass biolink:ChemicalEntityOrGeneOrGeneProduct . + +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 human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 8 ; + sh:order 2 ; sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; 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 6 ; + sh:path biolink:xref ], + [ sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:has_biological_sequence ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:class biolink:Zygosity ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_zygosity ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 8 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - 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 3 ; + sh:path biolink:in_taxon ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; + sh:order 7 ; sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:InformationContentEntity . + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:Genotype . -biolink:PhenotypicFeature a sh:NodeShape ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeature ; +biolink:SequenceVariant 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: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:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 2 ; + sh:path biolink:id ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 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 0 ; + sh:order 3 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 7 ; + 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:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 4 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - 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:order 12 ; + 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:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:path biolink:category ], + [ sh:description "The state of the sequence w.r.t a reference sequence" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 1 ; + 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:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:path biolink:provided_by ], + [ 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 12 ; + sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ] ; - sh:targetClass biolink:PhenotypicFeature . + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 8 ; + sh:path biolink:synonym ] ; + sh:targetClass biolink:SequenceVariant . biolink:ChemicalEntity a sh:NodeShape ; - rdfs:subClassOf biolink:NamedThing ; 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:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:property [ sh:datatype xsd:string ; + sh:description "" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], + sh:order 0 ; + sh:path biolink:trade_name ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path rdfs:label ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 1 ; sh:path biolink:available_from ], + [ sh:datatype xsd:boolean ; + sh:description "" ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:is_toxic ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 6 ; + sh:path biolink:xref ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 8 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - 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 "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: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:datatype xsd:string ; + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:max_tolerated_dose ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - 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 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:xref ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 14 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:boolean ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:is_toxic ], - [ sh:datatype xsd:string ; - sh:description "" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:trade_name ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 9 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ] ; + sh:path biolink:full_name ] ; sh:targetClass biolink:ChemicalEntity . -biolink:Gene a sh:NodeShape ; - rdfs:subClassOf biolink:BiologicalEntity ; +biolink:Agent 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:description "person, group, organization or project that provides a piece of information (i.e. a knowledge association)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + 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 "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; + sh:order 7 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Symbol for a particular thing" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:symbol ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:path biolink:full_name ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 11 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; + 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 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:has_biological_sequence ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 1 ; + sh:path biolink:address ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + 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:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; + sh:minCount 1 ; sh:order 6 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:Gene . - -biolink:DiseaseOrPhenotypicFeature a sh:NodeShape ; - rdfs:subClassOf biolink:BiologicalEntity ; - 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:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 9 ; + sh:path rdf:type ] ; + sh:targetClass biolink:Agent . + +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 database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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 5 ; + sh:path biolink:synonym ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; sh:order 6 ; sh:path biolink:id ], - [ 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 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - 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:DiseaseOrPhenotypicFeature . - -biolink:Disease a sh:NodeShape ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeature ; - 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:class biolink:Attribute ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ 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:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_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:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + 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:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:Disease . + sh:path biolink:provided_by ] ; + sh:targetClass biolink:PhenotypicFeature . -biolink:BiologicalSex a sh:NodeShape ; - rdfs:subClassOf biolink:Attribute ; +biolink:ChemicalRole a sh:NodeShape ; sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A role played by the molecular entity or part thereof within a chemical context." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "The 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:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - 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 13 ; - sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -36950,461 +30450,418 @@ biolink:BiologicalSex a sh:NodeShape ; 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 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 5 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], + 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 3 ; - sh:path biolink:has_qualitative_value ] ; - sh:targetClass biolink:BiologicalSex . - -biolink:BiologicalEntity a sh:NodeShape ; - rdfs:subClassOf biolink:NamedThing ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; + 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 7 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - 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 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 12 ; + sh:path dct:description ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 rdfs:label ], - [ sh:class biolink:Attribute ; + sh:path biolink:category ] ; + sh:targetClass biolink:ChemicalRole . + +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:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_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:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_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:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ 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:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; 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 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ] ; - sh:targetClass biolink:BiologicalEntity . - -biolink:AnatomicalEntity a sh:NodeShape ; - rdfs:subClassOf biolink:OrganismalEntity ; - sh:closed true ; - sh:description "A subcellular location, cell type or gross anatomical part" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - 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 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 7 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:DiseaseOrPhenotypicFeature . + +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 "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 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 0 ; + sh:order 4 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 8 ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 10 ; sh:path biolink:category ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 7 ; + 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 "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:has_biological_sequence ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 8 ; + 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 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:order 11 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + 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 biolink:in_taxon_label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 15 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; + sh:order 6 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:AnatomicalEntity . - -biolink:GeneOrGeneProduct a sh:NodeShape ; - rdfs:subClassOf biolink:MacromolecularMachineMixin ; - sh:closed false ; - sh:description "A union of gene loci or gene products. Frequently an identifier for one will be used as proxy for another" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:GeneOrGeneProduct . - -biolink:QuantityValue a sh:NodeShape ; - rdfs:subClassOf biolink:Annotation ; - sh:closed true ; - sh:description "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype ; - sh:description "connects a quantity value to a unit" ; + sh:description "Symbol for a particular thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path biolink:has_unit ], - [ sh:datatype xsd:double ; - sh:description "connects a quantity value to a number" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:has_numeric_value ] ; - sh:targetClass biolink:QuantityValue . + sh:path biolink:symbol ] ; + sh:targetClass biolink:Gene . -biolink:Association a sh:NodeShape ; - rdfs:subClassOf biolink:Entity ; +biolink:Disease a sh:NodeShape ; sh:closed true ; - sh:description "A typed association between two entities, supported by evidence" ; + 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:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 32 ; + sh:property [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:order 8 ; sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ 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 3 ; + 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:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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: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 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 18 ; - sh:path biolink:object_category ], + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; + sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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 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 10 ; + sh:path rdfs:label ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh: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:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:path biolink:iri ] ; + sh:targetClass biolink:Disease . + +biolink:BiologicalSex a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + 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:nodeKind sh:Literal ; - sh:order 34 ; + 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 36 ; + sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - 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:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "used to 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:Literal ; - 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 6 ; - sh:path biolink:publications ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ 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 attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this 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 1 ; + sh:path biolink:has_attribute_type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:description "Alternate human-readable names for a thing" ; sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 14 ; - 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:path biolink:deprecated ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 12 ; + sh:path dct:description ] ; + sh:targetClass biolink:BiologicalSex . + +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:datatype xsd:string ; + 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 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:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path biolink:aggregator_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:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "A unique 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 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - 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 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ 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 description of an entity" ; + sh:maxCount 1 ; + sh:order 11 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:in_taxon_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 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of 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 8 ; + sh:path biolink:category ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + 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 0 ; + sh:path biolink:in_taxon ] ; + sh:targetClass biolink:AnatomicalEntity . + +biolink:GeneOrGeneProduct a sh:NodeShape ; + sh:closed false ; + sh:description "A union of gene loci or gene products. Frequently an identifier for one will be used as proxy for another" ; + 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:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold 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 0 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:GeneOrGeneProduct . + +biolink:QuantityValue a sh:NodeShape ; + sh:closed true ; + sh:description "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "connects a quantity value to a unit" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 0 ; + sh:path biolink:has_unit ], + [ sh:datatype xsd:double ; + sh:description "connects a quantity value to a number" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:id ] ; - sh:targetClass biolink:Association . + sh:order 1 ; + sh:path biolink:has_numeric_value ] ; + sh:targetClass biolink:QuantityValue . biolink:OrganismTaxon a sh:NodeShape ; - rdfs:subClassOf biolink:NamedThing ; 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 ) ; @@ -37412,576 +30869,441 @@ biolink:OrganismTaxon a sh:NodeShape ; sh:description "A unique 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:Literal ; sh:order 5 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:class biolink:TaxonomicRank ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:iri ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_taxonomic_rank ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 4 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; + sh:order 3 ; + 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 2 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - 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 6 ; + sh:path biolink:iri ], + [ sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 7 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - 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:datatype xsd:string ; - sh:nodeKind sh:Literal ; 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:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path biolink:deprecated ], - [ sh:class biolink:TaxonomicRank ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_taxonomic_rank ], - [ 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:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:synonym ] ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:OrganismTaxon . -biolink:EvidenceType a sh:NodeShape ; - rdfs:subClassOf biolink:InformationContentEntity ; +biolink:NamedThing a sh:NodeShape ; sh:closed true ; - sh:description "Class of evidence that supports an association" ; + sh:description "a databased entity or concept/class" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh: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 "The value in this node property represents the knowledge provider that created or assembled the node 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:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:order 8 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; + sh:order 11 ; sh:path biolink:deprecated ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; + sh:order 7 ; sh:path rdf:type ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - 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 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:EvidenceType . - -biolink:RetrievalSource a sh:NodeShape ; - rdfs:subClassOf biolink:InformationContentEntity ; - 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:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 13 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:format ], + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; - sh:order 11 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:path biolink:id ], + [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - 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:path dct:description ], + [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path biolink:upstream_resource_ids ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + 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:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:deprecated ], - [ 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:order 5 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:NamedThing . + +biolink:EvidenceType a sh:NodeShape ; + sh:closed true ; + sh:description "Class of evidence that supports an association" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier 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:resource_role ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:creation_date ], + sh:order 8 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 14 ; + sh:order 11 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - 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:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 0 ; - sh:path biolink:resource_id ], + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; + sh:order 1 ; sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; 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 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 9 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:RetrievalSource . - -biolink:Publication a sh:NodeShape ; - rdfs:subClassOf biolink:InformationContentEntity ; - 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:datatype xsd:string ; - 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:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; + sh:order 13 ; sh:path dct:description ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:creation_date ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; + 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:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - 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:nodeKind sh:Literal ; sh:order 14 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 15 ; - sh:path biolink:iri ], + sh:path biolink:deprecated ], + [ sh:datatype xsd:date ; + 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:datatype xsd:string ; - 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:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:license ] ; + 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 "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; sh:order 18 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:license ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 21 ; sh:path biolink:deprecated ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:mesh_terms ], - [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:keywords ], + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:rights ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:summary ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:rights ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; + [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:category ], + [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:order 6 ; + sh:path dct:type ], + [ sh:datatype xsd:string ; + sh:order 17 ; + 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:datatype xsd:string ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; 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:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:pages ], + [ 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 19 ; + sh:path dct:description ], + [ sh:description "mesh terms tagging a publication" ; + sh:order 4 ; + sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + 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:nodeKind sh:Literal ; - sh:order 6 ; - sh:path dct:type ] ; + sh:order 14 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 "Alternate human-readable names for a thing" ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; + sh:order 3 ; + sh:path biolink:keywords ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:creation_date ] ; sh:targetClass biolink:Publication . -biolink:NamedThing a sh:NodeShape ; - rdfs:subClassOf biolink:Entity ; +biolink:RetrievalSource a sh:NodeShape ; sh:closed true ; - sh:description "a databased entity or concept/class" ; + 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:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; + sh:order 5 ; + 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 13 ; + sh:path biolink:category ], + [ sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path rdfs:label ], + [ sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:order 16 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - 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 10 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; + sh:order 18 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; + 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:maxCount 1 ; + sh:minCount 1 ; sh:order 1 ; - sh:path biolink:xref ], + sh:path biolink:resource_role ], + [ sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "A unique 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:Literal ; sh:order 4 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:Literal ; - sh:order 6 ; - sh:path biolink:category ], + sh:path biolink:license ], + [ sh:description "Alternate human-readable names for a thing" ; + sh:order 10 ; + sh:path biolink:synonym ], + [ 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:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 8 ; + 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:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], + sh:order 6 ; + sh:path biolink:format ], + [ sh:description "The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:resource_id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - 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 11 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 14 ; + sh:path rdf:type ], + [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ] ; - sh:targetClass biolink:NamedThing . + sh:order 12 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:RetrievalSource . biolink:Attribute a sh:NodeShape ; - rdfs:subClassOf biolink:NamedThing ; 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:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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 "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:Literal ; - sh:order 10 ; - sh:path biolink:category ], + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node 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 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique 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:Literal ; sh:order 5 ; 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. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such 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:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more 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:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:order 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:nodeKind sh:Literal ; sh:order 0 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 14 ; + sh:path biolink:deprecated ], [ 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:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - 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 13 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; + [ sh:description "Alternate human-readable names for a thing" ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - 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 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ] ; + sh:path biolink:has_quantitative_value ] ; sh:targetClass biolink:Attribute . biolink:OntologyClass a sh:NodeShape ; @@ -37992,7 +31314,6 @@ biolink:OntologyClass a sh:NodeShape ; sh:description "A unique 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:Literal ; sh:order 0 ; sh:path biolink:id ] ; sh:targetClass biolink:OntologyClass . diff --git a/project/shex/biolink_model.shex b/project/shex/biolink_model.shex index 10a169f21..95668c42a 100644 --- a/project/shex/biolink_model.shex +++ b/project/shex/biolink_model.shex @@ -1,5 +1,3 @@ -# metamodel_version: 1.7.0 -# version: 4.2.2 BASE PREFIX rdf: PREFIX rdfs: @@ -4330,3 +4328,4 @@ linkml:Sparqlpath xsd:string ) } + diff --git a/src/biolink_model/datamodel/model.py b/src/biolink_model/datamodel/model.py index 3869635e8..877717e8c 100644 --- a/src/biolink_model/datamodel/model.py +++ b/src/biolink_model/datamodel/model.py @@ -1,5 +1,5 @@ # Auto generated from biolink_model.yaml by pythongen.py version: 0.0.1 -# Generation date: 2024-09-23T16:45:09 +# Generation date: 2024-09-23T23:51:20 # Schema: Biolink-Model # # id: https://w3id.org/biolink/biolink-model @@ -11,7 +11,7 @@ from jsonasobj2 import JsonObj, as_dict from typing import Optional, List, Union, Dict, ClassVar, Any from dataclasses import dataclass -from datetime import date, datetime, time +from datetime import date, datetime from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions from linkml_runtime.utils.slot import Slot @@ -1383,7 +1383,7 @@ class OrganismTaxonToEnvironmentAssociationId(AssociationId): pass -@dataclass(repr=False) +@dataclass class MappingCollection(YAMLRoot): """ A collection of deprecated mappings. @@ -1405,7 +1405,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class PredicateMapping(YAMLRoot): """ A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should @@ -1512,7 +1512,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class OntologyClass(YAMLRoot): """ a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be @@ -1550,7 +1550,7 @@ class Annotation(YAMLRoot): class_model_uri: ClassVar[URIRef] = BIOLINK.Annotation -@dataclass(repr=False) +@dataclass class QuantityValue(Annotation): """ A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric @@ -1616,7 +1616,7 @@ class PathognomonicityQuantifier(SpecificityQuantifier): class_model_uri: ClassVar[URIRef] = BIOLINK.PathognomonicityQuantifier -@dataclass(repr=False) +@dataclass class FrequencyQuantifier(RelationshipQuantifier): _inherited_slots: ClassVar[List[str]] = [] @@ -1655,7 +1655,7 @@ class ChemicalOrDrugOrTreatment(YAMLRoot): class_model_uri: ClassVar[URIRef] = BIOLINK.ChemicalOrDrugOrTreatment -@dataclass(repr=False) +@dataclass class Entity(YAMLRoot): """ Root Biolink Model class for all things and informational relationships, real or imagined. @@ -1734,7 +1734,7 @@ def __new__(cls, *args, **kwargs): -@dataclass(repr=False) +@dataclass class NamedThing(Entity): """ a databased entity or concept/class @@ -1813,7 +1813,7 @@ def __new__(cls, *args, **kwargs): -@dataclass(repr=False) +@dataclass class Attribute(NamedThing): """ A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, @@ -1866,7 +1866,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ChemicalRole(Attribute): """ A role played by the molecular entity or part thereof within a chemical context. @@ -1896,7 +1896,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class BiologicalSex(Attribute): _inherited_slots: ClassVar[List[str]] = [] @@ -1923,7 +1923,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class PhenotypicSex(BiologicalSex): """ An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present. @@ -1953,7 +1953,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class GenotypicSex(BiologicalSex): """ An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex @@ -1984,7 +1984,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class SeverityValue(Attribute): """ describes the severity of a phenotypic feature or disease @@ -2014,7 +2014,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class RelationshipType(OntologyClass): """ An OWL property used as an edge label @@ -2037,7 +2037,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class TaxonomicRank(OntologyClass): """ A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom) @@ -2060,7 +2060,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class OrganismTaxon(NamedThing): """ A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). @@ -2094,7 +2094,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Event(NamedThing): """ Something that happens at a given place and time. @@ -2123,7 +2123,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class AdministrativeEntity(NamedThing): _inherited_slots: ClassVar[List[str]] = [] @@ -2145,7 +2145,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Agent(AdministrativeEntity): """ person, group, organization or project that provides a piece of information (i.e. a knowledge association) @@ -2187,7 +2187,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class InformationContentEntity(NamedThing): """ a piece of information that typically describes some topic of discourse or is used as support. @@ -2227,7 +2227,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class StudyResult(InformationContentEntity): """ A collection of data items from a study that are about a particular study subject or experimental unit (the @@ -2254,7 +2254,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class StudyVariable(InformationContentEntity): """ a variable that is used as a measure in the investigation of a study @@ -2283,7 +2283,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class CommonDataElement(InformationContentEntity): """ A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable @@ -2314,7 +2314,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ConceptCountAnalysisResult(StudyResult): """ A result of a concept count analysis. @@ -2343,7 +2343,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ObservedExpectedFrequencyAnalysisResult(StudyResult): """ A result of a observed expected frequency analysis. @@ -2372,7 +2372,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class RelativeFrequencyAnalysisResult(StudyResult): """ A result of a relative frequency analysis. @@ -2401,7 +2401,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class TextMiningResult(StudyResult): """ A result of text mining. @@ -2430,7 +2430,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ChiSquaredAnalysisResult(StudyResult): """ A result of a chi squared analysis. @@ -2459,7 +2459,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class LogOddsAnalysisResult(StudyResult): """ A result of a log odds ratio analysis. @@ -2488,7 +2488,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Dataset(InformationContentEntity): """ an item that refers to a collection of data from a data source. @@ -2517,7 +2517,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class DatasetDistribution(InformationContentEntity): """ an item that holds distribution level information about a dataset. @@ -2550,7 +2550,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class DatasetVersion(InformationContentEntity): """ an item that holds version level information about a dataset. @@ -2591,7 +2591,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class DatasetSummary(InformationContentEntity): """ an item that holds summary level information about a dataset. @@ -2628,7 +2628,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ConfidenceLevel(InformationContentEntity): """ Level of confidence in a statement @@ -2657,7 +2657,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class EvidenceType(InformationContentEntity): """ Class of evidence that supports an association @@ -2686,7 +2686,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Publication(InformationContentEntity): """ Any ‘published’ piece of information. Publications are considered broadly to include any document or document part @@ -2759,7 +2759,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Book(Publication): """ This class may rarely be instantiated except if use cases of a given knowledge graph support its utility. @@ -2794,7 +2794,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class BookChapter(Publication): _inherited_slots: ClassVar[List[str]] = [] @@ -2835,7 +2835,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Serial(Publication): """ This class may rarely be instantiated except if use cases of a given knowledge graph support its utility. @@ -2882,7 +2882,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Article(Publication): """ a piece of writing on a particular topic presented as a stand-alone section of a larger publication @@ -2930,7 +2930,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class JournalArticle(Article): """ an article, typically presenting results of research, that is published in an issue of a scientific journal. @@ -2961,7 +2961,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Patent(Publication): """ a legal document granted by a patent issuing authority which confers upon the patenter the sole right to make, use @@ -2992,7 +2992,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class WebPage(Publication): """ a document that is published according to World Wide Web standards, which may incorporate text, graphics, sound, @@ -3023,7 +3023,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class PreprintPublication(Publication): """ a document reresenting an early version of an author's original scholarly work, such as a research paper or a @@ -3054,7 +3054,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class DrugLabel(Publication): """ a document accompanying a drug or its container that provides written, printed or graphic information about the @@ -3086,7 +3086,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class RetrievalSource(InformationContentEntity): """ Provides information about how a particular InformationResource served as a source from which knowledge expressed @@ -3161,7 +3161,7 @@ class PhysicalEssence(PhysicalEssenceOrOccurrent): class_model_uri: ClassVar[URIRef] = BIOLINK.PhysicalEssence -@dataclass(repr=False) +@dataclass class PhysicalEntity(NamedThing): """ An entity that has material reality (a.k.a. physical essence). @@ -3214,7 +3214,7 @@ class ActivityAndBehavior(Occurrent): class_model_uri: ClassVar[URIRef] = BIOLINK.ActivityAndBehavior -@dataclass(repr=False) +@dataclass class Activity(NamedThing): """ An activity is something that occurs over a period of time and acts upon or with entities; it may include @@ -3244,7 +3244,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Study(Activity): """ a detailed investigation and/or analysis @@ -3273,7 +3273,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Procedure(NamedThing): """ A series of actions conducted in a certain order or manner @@ -3302,7 +3302,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Phenomenon(NamedThing): """ a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question @@ -3331,7 +3331,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Device(NamedThing): """ A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment @@ -3360,7 +3360,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class DiagnosticAid(NamedThing): """ A device or substance used to help diagnose disease or injury @@ -3401,7 +3401,7 @@ class SubjectOfInvestigation(YAMLRoot): class_model_uri: ClassVar[URIRef] = BIOLINK.SubjectOfInvestigation -@dataclass(repr=False) +@dataclass class MaterialSample(PhysicalEntity): """ A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a @@ -3432,7 +3432,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class PlanetaryEntity(NamedThing): """ Any entity or process that exists at the level of the whole planet @@ -3461,7 +3461,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class EnvironmentalProcess(PlanetaryEntity): _inherited_slots: ClassVar[List[str]] = [] @@ -3487,7 +3487,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class EnvironmentalFeature(PlanetaryEntity): _inherited_slots: ClassVar[List[str]] = [] @@ -3513,7 +3513,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class GeographicLocation(PlanetaryEntity): """ a location that can be described in lat/long coordinates @@ -3550,7 +3550,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class GeographicLocationAtTime(GeographicLocation): """ a location that can be described in lat/long coordinates, for a particular time @@ -3583,7 +3583,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ThingWithTaxon(YAMLRoot): """ A mixin that can be used on any entity that can be taxonomically classified. This includes individual organisms; @@ -3610,7 +3610,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class BiologicalEntity(NamedThing): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -3640,7 +3640,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class GenomicEntity(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] @@ -3658,7 +3658,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class EpigenomicEntity(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] @@ -3676,7 +3676,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class ChemicalEntity(NamedThing): """ A chemical entity is a physical entity that pertains to chemistry or biochemistry. @@ -3727,7 +3727,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class MolecularEntity(ChemicalEntity): """ A molecular entity is a chemical entity composed of individual or covalently bonded atoms. @@ -3760,7 +3760,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class SmallMolecule(MolecularEntity): """ A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, @@ -3792,7 +3792,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ChemicalMixture(ChemicalEntity): """ A chemical mixture is a chemical entity composed of two or more molecular entities. @@ -3838,7 +3838,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class NucleicAcidEntity(MolecularEntity): """ A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based @@ -3882,7 +3882,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class RegulatoryRegion(BiologicalEntity): """ A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- @@ -3916,7 +3916,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class AccessibleDnaRegion(RegulatoryRegion): """ A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as @@ -3950,7 +3950,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class TranscriptionFactorBindingSite(RegulatoryRegion): """ A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that @@ -3984,7 +3984,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class MolecularMixture(ChemicalMixture): """ A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and @@ -4014,7 +4014,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ComplexMolecularMixture(ChemicalMixture): """ A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown @@ -4044,7 +4044,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class BiologicalProcessOrActivity(BiologicalEntity): """ Either an individual molecular activity, or a collection of causally connected molecular activities in a @@ -4089,7 +4089,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class MolecularActivity(BiologicalProcessOrActivity): """ An execution of a molecular function carried out by a gene product or macromolecular complex. @@ -4133,7 +4133,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class BiologicalProcess(BiologicalProcessOrActivity): """ One or more causally connected executions of molecular functions @@ -4162,7 +4162,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Pathway(BiologicalProcess): _inherited_slots: ClassVar[List[str]] = ["in_taxon", "has_input", "has_output", "enabled_by"] @@ -4188,7 +4188,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class PhysiologicalProcess(BiologicalProcess): _inherited_slots: ClassVar[List[str]] = ["in_taxon", "has_input", "has_output", "enabled_by"] @@ -4214,7 +4214,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Behavior(BiologicalProcess): _inherited_slots: ClassVar[List[str]] = ["in_taxon", "has_input", "has_output", "enabled_by"] @@ -4240,7 +4240,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ProcessedMaterial(ChemicalMixture): """ A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a @@ -4270,7 +4270,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Drug(MolecularMixture): """ A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease @@ -4299,7 +4299,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class EnvironmentalFoodContaminant(ChemicalEntity): _inherited_slots: ClassVar[List[str]] = ["has_chemical_role"] @@ -4325,7 +4325,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class FoodAdditive(ChemicalEntity): _inherited_slots: ClassVar[List[str]] = ["has_chemical_role"] @@ -4351,7 +4351,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Food(ChemicalMixture): """ A substance consumed by a living organism as a source of nutrition @@ -4380,7 +4380,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class OrganismAttribute(Attribute): """ describes a characteristic of an organismal entity. @@ -4410,7 +4410,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class PhenotypicQuality(OrganismAttribute): """ A property of a phenotype @@ -4440,7 +4440,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class GeneticInheritance(BiologicalEntity): """ The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, @@ -4470,7 +4470,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class OrganismalEntity(BiologicalEntity): """ A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding @@ -4500,7 +4500,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Bacterium(OrganismalEntity): """ A member of a group of unicellular microorganisms lacking a nuclear membrane, that reproduce by binary fission and @@ -4530,7 +4530,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Virus(OrganismalEntity): """ A virus is a microorganism that replicates itself as a microRNA and infects the host cell. @@ -4559,7 +4559,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class CellularOrganism(OrganismalEntity): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -4585,7 +4585,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Mammal(CellularOrganism): """ A member of the class Mammalia, a clade of endothermic amniotes distinguished from reptiles and birds by the @@ -4615,7 +4615,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Human(Mammal): """ A member of the the species Homo sapiens. @@ -4644,7 +4644,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Plant(CellularOrganism): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -4670,7 +4670,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Invertebrate(CellularOrganism): """ An animal lacking a vertebral column. This group consists of 98% of all animal species. @@ -4699,7 +4699,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Vertebrate(CellularOrganism): """ A sub-phylum of animals consisting of those having a bony or cartilaginous vertebral column. @@ -4728,7 +4728,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Fungus(CellularOrganism): """ A kingdom of eukaryotic, heterotrophic organisms that live as saprobes or parasites, including mushrooms, yeasts, @@ -4759,7 +4759,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class LifeStage(OrganismalEntity): """ A stage of development or growth of an organism, including post-natal adult stages @@ -4788,7 +4788,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class IndividualOrganism(OrganismalEntity): """ An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: @@ -4818,7 +4818,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class PopulationOfIndividualOrganisms(OrganismalEntity): """ A collection of individuals from the same taxonomic class distinguished by one or more characteristics. @@ -4848,7 +4848,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class StudyPopulation(PopulationOfIndividualOrganisms): """ A group of people banded together or treated as a group as participants in a research study. @@ -4877,7 +4877,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class DiseaseOrPhenotypicFeature(BiologicalEntity): """ Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these @@ -4909,7 +4909,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Disease(DiseaseOrPhenotypicFeature): """ A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that @@ -4940,7 +4940,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class PhenotypicFeature(DiseaseOrPhenotypicFeature): """ A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an @@ -4970,7 +4970,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class BehavioralFeature(PhenotypicFeature): """ A phenotypic feature which is behavioral in nature. @@ -4999,7 +4999,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class AnatomicalEntity(OrganismalEntity): """ A subcellular location, cell type or gross anatomical part @@ -5028,7 +5028,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class CellularComponent(AnatomicalEntity): """ A location in or around a cell @@ -5057,7 +5057,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Cell(AnatomicalEntity): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -5083,7 +5083,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class CellLine(OrganismalEntity): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -5109,7 +5109,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class GrossAnatomicalStructure(AnatomicalEntity): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -5161,7 +5161,7 @@ class ChemicalEntityOrProteinOrPolypeptide(YAMLRoot): class_model_uri: ClassVar[URIRef] = BIOLINK.ChemicalEntityOrProteinOrPolypeptide -@dataclass(repr=False) +@dataclass class MacromolecularMachineMixin(YAMLRoot): """ A union of gene locus, gene product, and macromolecular complex. These are the basic units of function in a cell. @@ -5195,7 +5195,7 @@ class GeneOrGeneProduct(MacromolecularMachineMixin): class_model_uri: ClassVar[URIRef] = BIOLINK.GeneOrGeneProduct -@dataclass(repr=False) +@dataclass class Gene(BiologicalEntity): """ A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A @@ -5242,7 +5242,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class GeneProductMixin(GeneOrGeneProduct): """ The functional molecular product of a single gene locus. Gene products are either proteins or functional RNA @@ -5284,7 +5284,7 @@ class GeneProductIsoformMixin(GeneProductMixin): class_model_uri: ClassVar[URIRef] = BIOLINK.GeneProductIsoformMixin -@dataclass(repr=False) +@dataclass class MacromolecularComplex(BiologicalEntity): """ A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which @@ -5318,7 +5318,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class NucleosomeModification(BiologicalEntity): """ A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a @@ -5366,7 +5366,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Genome(BiologicalEntity): """ A genome is the sum of genetic material within a cell or virion. @@ -5399,7 +5399,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Exon(BiologicalEntity): """ A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA @@ -5429,7 +5429,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Transcript(BiologicalEntity): """ An RNA synthesized on a DNA or RNA template by an RNA polymerase. @@ -5458,7 +5458,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class CodingSequence(BiologicalEntity): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -5488,7 +5488,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Polypeptide(BiologicalEntity): """ A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based @@ -5519,7 +5519,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Protein(Polypeptide): """ A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated @@ -5563,7 +5563,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ProteinIsoform(Protein): """ Represents a protein that is a specific isoform of the canonical or reference protein. See @@ -5607,7 +5607,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ProteinDomain(BiologicalEntity): """ A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently @@ -5643,7 +5643,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class PosttranslationalModification(BiologicalEntity): """ A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to @@ -5687,7 +5687,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ProteinFamily(BiologicalEntity): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -5718,7 +5718,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class NucleicAcidSequenceMotif(BiologicalEntity): """ A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological @@ -5748,7 +5748,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class RNAProduct(Transcript): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -5788,7 +5788,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class RNAProductIsoform(RNAProduct): """ Represents a protein that is a specific isoform of the canonical or reference RNA @@ -5831,7 +5831,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class NoncodingRNAProduct(RNAProduct): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -5857,7 +5857,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class MicroRNA(NoncodingRNAProduct): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -5883,7 +5883,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class SiRNA(NoncodingRNAProduct): """ A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular @@ -5914,7 +5914,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class GeneGroupingMixin(YAMLRoot): """ any grouping of multiple genes or gene products @@ -5936,7 +5936,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class GeneFamily(BiologicalEntity): """ any grouping of multiple genes or gene products related by common descent @@ -5970,7 +5970,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Zygosity(Attribute): _inherited_slots: ClassVar[List[str]] = [] @@ -5997,7 +5997,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Genotype(BiologicalEntity): """ An information content entity that describes a genome by specifying the total variation in genomic sequence and/or @@ -6035,7 +6035,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Haplotype(BiologicalEntity): """ A set of zero or more Alleles on a single instance of a Sequence[VMC] @@ -6068,7 +6068,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class SequenceVariant(BiologicalEntity): """ A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. @@ -6106,7 +6106,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Snv(SequenceVariant): """ SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist @@ -6135,7 +6135,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ReagentTargetedGene(BiologicalEntity): """ A gene altered in its expression level in the context of some experiment as a result of being targeted by @@ -6169,7 +6169,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ClinicalAttribute(Attribute): """ Attributes relating to a clinical manifestation @@ -6199,7 +6199,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ClinicalMeasurement(ClinicalAttribute): """ A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject @@ -6235,7 +6235,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ClinicalModifier(ClinicalAttribute): """ Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, @@ -6266,7 +6266,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ClinicalCourse(ClinicalAttribute): """ The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the @@ -6297,7 +6297,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Onset(ClinicalCourse): """ The age group in which (disease) symptom manifestations appear. @@ -6327,7 +6327,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ClinicalEntity(NamedThing): """ Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed @@ -6357,7 +6357,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ClinicalTrial(ClinicalEntity): _inherited_slots: ClassVar[List[str]] = [] @@ -6383,7 +6383,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ClinicalIntervention(ClinicalEntity): _inherited_slots: ClassVar[List[str]] = [] @@ -6409,7 +6409,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ClinicalFinding(PhenotypicFeature): """ this category is currently considered broad enough to tag clinical lab measurements and other biological @@ -6444,7 +6444,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Hospitalization(ClinicalIntervention): _inherited_slots: ClassVar[List[str]] = [] @@ -6470,7 +6470,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class SocioeconomicAttribute(Attribute): """ Attributes relating to a socioeconomic manifestation @@ -6500,7 +6500,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Case(IndividualOrganism): """ An individual (human) organism that has a patient role in some clinical context. @@ -6529,7 +6529,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Cohort(StudyPopulation): """ A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a @@ -6559,7 +6559,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ExposureEvent(OntologyClass): """ A (possibly time bounded) incidence of a feature of the environment of an organism that influences one or more @@ -6582,7 +6582,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class GenomicBackgroundExposure(Attribute): """ A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or @@ -6648,7 +6648,7 @@ class PathologicalEntityMixin(YAMLRoot): class_model_uri: ClassVar[URIRef] = BIOLINK.PathologicalEntityMixin -@dataclass(repr=False) +@dataclass class PathologicalProcess(BiologicalProcess): """ A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, @@ -6678,7 +6678,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class PathologicalProcessExposure(Attribute): """ A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an @@ -6713,7 +6713,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class PathologicalAnatomicalStructure(AnatomicalEntity): """ An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, @@ -6743,7 +6743,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class PathologicalAnatomicalExposure(Attribute): """ An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or @@ -6778,7 +6778,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class DiseaseOrPhenotypicFeatureExposure(Attribute): """ A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or @@ -6814,7 +6814,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ChemicalExposure(Attribute): """ A chemical exposure is an intake of a particular chemical entity. @@ -6853,7 +6853,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ComplexChemicalExposure(Attribute): """ A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug. @@ -6883,7 +6883,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class DrugExposure(ChemicalExposure): """ A drug exposure is an intake of a particular drug. @@ -6917,7 +6917,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class DrugToGeneInteractionExposure(DrugExposure): """ drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are @@ -6953,7 +6953,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class Treatment(NamedThing): """ A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices @@ -7002,7 +7002,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class BioticExposure(Attribute): """ An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses). @@ -7036,7 +7036,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class EnvironmentalExposure(Attribute): """ A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), @@ -7071,7 +7071,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class GeographicExposure(EnvironmentalExposure): """ A geographic exposure is a factor relating to geographic proximity to some impactful entity. @@ -7105,7 +7105,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class BehavioralExposure(Attribute): """ A behavioral exposure is a factor relating to behavior impacting an individual. @@ -7139,7 +7139,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class SocioeconomicExposure(Attribute): """ A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. @@ -7293,7 +7293,7 @@ class SocioeconomicOutcome(YAMLRoot): class_model_uri: ClassVar[URIRef] = BIOLINK.SocioeconomicOutcome -@dataclass(repr=False) +@dataclass class Association(Entity): """ A typed association between two entities, supported by evidence @@ -7309,8 +7309,8 @@ class Association(Entity): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" negated: Optional[Union[bool, Bool]] = None qualifier: Optional[str] = None qualifiers: Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]] = empty_list() @@ -7495,7 +7495,7 @@ def __new__(cls, *args, **kwargs): -@dataclass(repr=False) +@dataclass class ChemicalEntityAssessesNamedThingAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -7508,8 +7508,8 @@ class ChemicalEntityAssessesNamedThingAssociation(Association): subject: Union[str, ChemicalEntityId] = None object: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -7538,7 +7538,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ContributorAssociation(Association): """ Any association between an entity (such as a publication) and various agents that contribute to its realisation @@ -7554,8 +7554,8 @@ class ContributorAssociation(Association): subject: Union[str, InformationContentEntityId] = None predicate: Union[str, PredicateType] = None object: Union[str, AgentId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" qualifiers: Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]] = empty_list() def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -7589,7 +7589,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class GenotypeToGenotypePartAssociation(Association): """ Any association between one genotype and a genotypic entity that is a sub-component of it @@ -7605,8 +7605,8 @@ class GenotypeToGenotypePartAssociation(Association): predicate: Union[str, PredicateType] = None subject: Union[str, GenotypeId] = None object: Union[str, GenotypeId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -7635,7 +7635,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class GenotypeToGeneAssociation(Association): """ Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single @@ -7652,8 +7652,8 @@ class GenotypeToGeneAssociation(Association): predicate: Union[str, PredicateType] = None subject: Union[str, GenotypeId] = None object: Union[str, GeneId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -7682,7 +7682,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class GenotypeToVariantAssociation(Association): """ Any association between a genotype and a sequence variant. @@ -7698,8 +7698,8 @@ class GenotypeToVariantAssociation(Association): predicate: Union[str, PredicateType] = None subject: Union[str, GenotypeId] = None object: Union[str, SequenceVariantId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -7728,7 +7728,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class GeneToGeneAssociation(Association): """ abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes @@ -7745,8 +7745,8 @@ class GeneToGeneAssociation(Association): predicate: Union[str, PredicateType] = None subject: Union[dict, GeneOrGeneProduct] = None object: Union[dict, GeneOrGeneProduct] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.subject): @@ -7765,7 +7765,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class GeneToGeneHomologyAssociation(GeneToGeneAssociation): """ A homology association between two genes. May be orthology (in which case the species of subject and object should @@ -7782,8 +7782,8 @@ class GeneToGeneHomologyAssociation(GeneToGeneAssociation): subject: Union[dict, GeneOrGeneProduct] = None predicate: Union[str, PredicateType] = None object: Union[dict, GeneOrGeneProduct] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -7812,7 +7812,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class GeneToGeneFamilyAssociation(Association): """ Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence @@ -7830,8 +7830,8 @@ class GeneToGeneFamilyAssociation(Association): subject: Union[str, GeneId] = None object: Union[str, GeneFamilyId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -7860,7 +7860,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class GeneExpressionMixin(YAMLRoot): """ Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the @@ -7894,7 +7894,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class GeneToGeneCoexpressionAssociation(GeneToGeneAssociation): """ Indicates that two genes are co-expressed, generally under the same conditions. @@ -7910,8 +7910,8 @@ class GeneToGeneCoexpressionAssociation(GeneToGeneAssociation): subject: Union[dict, GeneOrGeneProduct] = None object: Union[dict, GeneOrGeneProduct] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" quantifier_qualifier: Optional[Union[str, OntologyClassId]] = None expression_site: Optional[Union[str, AnatomicalEntityId]] = None stage_qualifier: Optional[Union[str, LifeStageId]] = None @@ -7946,7 +7946,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class PairwiseGeneToGeneInteraction(GeneToGeneAssociation): """ An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between @@ -7963,8 +7963,8 @@ class PairwiseGeneToGeneInteraction(GeneToGeneAssociation): subject: Union[dict, GeneOrGeneProduct] = None object: Union[dict, GeneOrGeneProduct] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -7983,7 +7983,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class PairwiseMolecularInteraction(PairwiseGeneToGeneInteraction): """ An interaction at the molecular level between two physical entities @@ -7999,8 +7999,8 @@ class PairwiseMolecularInteraction(PairwiseGeneToGeneInteraction): subject: Union[str, MolecularEntityId] = None predicate: Union[str, PredicateType] = None object: Union[str, MolecularEntityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" interacting_molecules_category: Optional[Union[str, OntologyClassId]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -8033,7 +8033,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class CellLineToEntityAssociationMixin(YAMLRoot): """ An relationship between a cell line and another entity @@ -8068,7 +8068,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class CellLineToDiseaseOrPhenotypicFeatureAssociation(Association): """ An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an @@ -8085,8 +8085,8 @@ class CellLineToDiseaseOrPhenotypicFeatureAssociation(Association): predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None subject: Union[str, DiseaseOrPhenotypicFeatureId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -8115,7 +8115,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ChemicalEntityToEntityAssociationMixin(YAMLRoot): """ An interaction between a chemical entity and another entity @@ -8150,7 +8150,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class DrugToEntityAssociationMixin(ChemicalEntityToEntityAssociationMixin): """ An interaction between a drug and another entity @@ -8190,7 +8190,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class ChemicalToEntityAssociationMixin(ChemicalEntityToEntityAssociationMixin): """ An interaction between a chemical entity and another entity @@ -8230,7 +8230,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class CaseToEntityAssociationMixin(YAMLRoot): """ An abstract association for use where the case is the subject @@ -8265,7 +8265,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class ChemicalToChemicalAssociation(Association): """ A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal @@ -8282,8 +8282,8 @@ class ChemicalToChemicalAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, ChemicalEntityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -8312,7 +8312,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ReactionToParticipantAssociation(ChemicalToChemicalAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -8325,8 +8325,8 @@ class ReactionToParticipantAssociation(ChemicalToChemicalAssociation): predicate: Union[str, PredicateType] = None object: Union[str, ChemicalEntityId] = None subject: Union[str, MolecularEntityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" stoichiometry: Optional[int] = None reaction_direction: Optional[Union[str, "ReactionDirectionEnum"]] = None reaction_side: Optional[Union[str, "ReactionSideEnum"]] = None @@ -8357,7 +8357,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ReactionToCatalystAssociation(ReactionToParticipantAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -8370,8 +8370,8 @@ class ReactionToCatalystAssociation(ReactionToParticipantAssociation): predicate: Union[str, PredicateType] = None subject: Union[str, MolecularEntityId] = None object: Union[dict, GeneOrGeneProduct] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -8390,7 +8390,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ChemicalToChemicalDerivationAssociation(ChemicalToChemicalAssociation): """ A causal relationship between two chemical entities, where the subject represents the upstream entity and the @@ -8408,8 +8408,8 @@ class ChemicalToChemicalDerivationAssociation(ChemicalToChemicalAssociation): subject: Union[str, ChemicalEntityId] = None object: Union[str, ChemicalEntityId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" catalyst_qualifier: Optional[Union[Union[dict, MacromolecularMachineMixin], List[Union[dict, MacromolecularMachineMixin]]]] = empty_list() def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -8443,7 +8443,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ChemicalToDiseaseOrPhenotypicFeatureAssociation(Association): """ An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise @@ -8460,8 +8460,8 @@ class ChemicalToDiseaseOrPhenotypicFeatureAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, DiseaseOrPhenotypicFeatureId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -8490,7 +8490,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation(Association): """ This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic @@ -8507,8 +8507,8 @@ class ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation(Associati subject: Union[str, NamedThingId] = None object: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" FDA_adverse_event_level: Optional[Union[str, "FDAIDAAdverseEventEnum"]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -8541,7 +8541,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation(ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation): """ This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic @@ -8558,8 +8558,8 @@ class ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation(C subject: Union[str, NamedThingId] = None object: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -8588,7 +8588,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class GeneToPathwayAssociation(Association): """ An interaction between a gene or gene product and a biological process or pathway. @@ -8604,8 +8604,8 @@ class GeneToPathwayAssociation(Association): predicate: Union[str, PredicateType] = None subject: Union[dict, GeneOrGeneProduct] = None object: Union[str, PathwayId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -8634,7 +8634,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class MolecularActivityToPathwayAssociation(Association): """ Association that holds the relationship between a reaction and the pathway it participates in. @@ -8650,8 +8650,8 @@ class MolecularActivityToPathwayAssociation(Association): subject: Union[str, MolecularActivityId] = None object: Union[str, PathwayId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -8680,7 +8680,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ChemicalToPathwayAssociation(Association): """ An interaction between a chemical entity and a biological process or pathway. @@ -8696,8 +8696,8 @@ class ChemicalToPathwayAssociation(Association): predicate: Union[str, PredicateType] = None subject: Union[str, ChemicalEntityId] = None object: Union[str, PathwayId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -8726,7 +8726,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class NamedThingAssociatedWithLikelihoodOfNamedThingAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -8739,8 +8739,8 @@ class NamedThingAssociatedWithLikelihoodOfNamedThingAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" subject_aspect_qualifier: Optional[str] = None subject_context_qualifier: Optional[Union[str, OntologyClassId]] = None object_aspect_qualifier: Optional[str] = None @@ -8789,7 +8789,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ChemicalGeneInteractionAssociation(Association): """ describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical @@ -8807,8 +8807,8 @@ class ChemicalGeneInteractionAssociation(Association): subject: Union[str, ChemicalEntityId] = None object: Union[dict, GeneOrGeneProduct] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" subject_form_or_variant_qualifier: Optional[Union[str, "ChemicalOrGeneOrGeneProductFormOrVariantEnum"]] = None subject_part_qualifier: Optional[Union[str, "GeneOrGeneProductOrChemicalPartQualifierEnum"]] = None subject_derivative_qualifier: Optional[Union[str, "ChemicalEntityDerivativeEnum"]] = None @@ -8869,7 +8869,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class GeneRegulatesGeneAssociation(Association): """ Describes a regulatory relationship between two genes or gene products. @@ -8888,8 +8888,8 @@ class GeneRegulatesGeneAssociation(Association): subject: Union[dict, GeneOrGeneProduct] = None predicate: Union[str, PredicateType] = None object: Union[dict, GeneOrGeneProduct] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" species_context_qualifier: Optional[Union[str, OrganismTaxonId]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -8937,7 +8937,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ProcessRegulatesProcessAssociation(Association): """ Describes a regulatory relationship between two genes or gene products. @@ -8953,8 +8953,8 @@ class ProcessRegulatesProcessAssociation(Association): subject: Union[str, BiologicalProcessId] = None predicate: Union[str, PredicateType] = None object: Union[str, BiologicalProcessId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -8983,7 +8983,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ChemicalAffectsGeneAssociation(Association): """ Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, @@ -9000,8 +9000,8 @@ class ChemicalAffectsGeneAssociation(Association): subject: Union[str, ChemicalEntityId] = None predicate: Union[str, PredicateType] = None object: Union[dict, GeneOrGeneProduct] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" subject_form_or_variant_qualifier: Optional[Union[str, "ChemicalOrGeneOrGeneProductFormOrVariantEnum"]] = None subject_part_qualifier: Optional[Union[str, "GeneOrGeneProductOrChemicalPartQualifierEnum"]] = None subject_derivative_qualifier: Optional[Union[str, "ChemicalEntityDerivativeEnum"]] = None @@ -9090,7 +9090,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class GeneAffectsChemicalAssociation(Association): """ Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, @@ -9107,8 +9107,8 @@ class GeneAffectsChemicalAssociation(Association): subject: Union[dict, GeneOrGeneProduct] = None predicate: Union[str, PredicateType] = None object: Union[str, ChemicalEntityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" subject_form_or_variant_qualifier: Optional[Union[str, "ChemicalOrGeneOrGeneProductFormOrVariantEnum"]] = None subject_part_qualifier: Optional[Union[str, "GeneOrGeneProductOrChemicalPartQualifierEnum"]] = None subject_derivative_qualifier: Optional[str] = None @@ -9201,7 +9201,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class DrugToGeneAssociation(Association): """ An interaction between a drug and a gene or gene product. @@ -9217,8 +9217,8 @@ class DrugToGeneAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[dict, GeneOrGeneProduct] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -9247,7 +9247,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class MaterialSampleToEntityAssociationMixin(YAMLRoot): """ An association between a material sample and something. @@ -9282,7 +9282,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class MaterialSampleDerivationAssociation(Association): """ An association between a material sample and the material entity from which it is derived. @@ -9298,8 +9298,8 @@ class MaterialSampleDerivationAssociation(Association): subject: Union[str, MaterialSampleId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -9328,7 +9328,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class MaterialSampleToDiseaseOrPhenotypicFeatureAssociation(Association): """ An association between a material sample and a disease or phenotype. @@ -9344,8 +9344,8 @@ class MaterialSampleToDiseaseOrPhenotypicFeatureAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -9374,7 +9374,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class DiseaseToEntityAssociationMixin(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] @@ -9406,7 +9406,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class EntityToExposureEventAssociationMixin(YAMLRoot): """ An association between some entity and an exposure event. @@ -9441,7 +9441,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class DiseaseToExposureEventAssociation(Association): """ An association between an exposure event and a disease. @@ -9457,8 +9457,8 @@ class DiseaseToExposureEventAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -9487,7 +9487,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class EntityToOutcomeAssociationMixin(YAMLRoot): """ An association between some entity and an outcome @@ -9522,7 +9522,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class ExposureEventToOutcomeAssociation(Association): """ An association between an exposure event and an outcome. @@ -9538,8 +9538,8 @@ class ExposureEventToOutcomeAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" population_context_qualifier: Optional[Union[str, PopulationOfIndividualOrganismsId]] = None temporal_context_qualifier: Optional[Union[str, TimeType]] = None @@ -9576,7 +9576,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class FrequencyQualifierMixin(YAMLRoot): """ Qualifier for frequency type associations @@ -9615,7 +9615,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class EntityToFeatureOrDiseaseQualifiersMixin(FrequencyQualifierMixin): """ Qualifiers for entity to disease or phenotype associations. @@ -9655,7 +9655,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class FeatureOrDiseaseQualifiersToEntityMixin(FrequencyQualifierMixin): """ Qualifiers for disease or phenotype to entity associations. @@ -9695,7 +9695,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class EntityToPhenotypicFeatureAssociationMixin(EntityToFeatureOrDiseaseQualifiersMixin): _inherited_slots: ClassVar[List[str]] = [] @@ -9747,7 +9747,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class PhenotypicFeatureToEntityAssociationMixin(FeatureOrDiseaseQualifiersToEntityMixin): _inherited_slots: ClassVar[List[str]] = [] @@ -9789,7 +9789,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class PhenotypicFeatureToPhenotypicFeatureAssociation(Association): """ Association between two concept nodes of phenotypic character, qualified by the predicate used. This association @@ -9806,8 +9806,8 @@ class PhenotypicFeatureToPhenotypicFeatureAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -9864,7 +9864,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class InformationContentEntityToNamedThingAssociation(Association): """ association between a named thing and a information content entity where the specific context of the relationship @@ -9885,8 +9885,8 @@ class InformationContentEntityToNamedThingAssociation(Association): subject: Union[str, NamedThingId] = None object: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -9915,7 +9915,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class EntityToDiseaseAssociationMixin(EntityToFeatureOrDiseaseQualifiersMixin): """ mixin class for any association whose object (target node) is a disease @@ -9940,7 +9940,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class DiseaseOrPhenotypicFeatureToEntityAssociationMixin(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] @@ -9972,7 +9972,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class DiseaseOrPhenotypicFeatureToLocationAssociation(Association): """ An association between either a disease or a phenotypic feature and an anatomical entity, where the @@ -9989,8 +9989,8 @@ class DiseaseOrPhenotypicFeatureToLocationAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, AnatomicalEntityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -10019,7 +10019,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation(Association): """ An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance. @@ -10035,8 +10035,8 @@ class DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, GeneticInheritanceId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -10065,7 +10065,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class EntityToDiseaseOrPhenotypicFeatureAssociationMixin(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] @@ -10097,7 +10097,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class GenotypeToEntityAssociationMixin(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] @@ -10129,7 +10129,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class GenotypeToPhenotypicFeatureAssociation(Association): """ Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, @@ -10146,8 +10146,8 @@ class GenotypeToPhenotypicFeatureAssociation(Association): object: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None subject: Union[str, GenotypeId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -10204,7 +10204,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ExposureEventToPhenotypicFeatureAssociation(Association): """ Any association between an environment and a phenotypic feature, where being in the environment influences the @@ -10221,8 +10221,8 @@ class ExposureEventToPhenotypicFeatureAssociation(Association): predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None subject: Union[str, ExposureEventId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -10279,7 +10279,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class DiseaseToPhenotypicFeatureAssociation(Association): """ An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the @@ -10296,8 +10296,8 @@ class DiseaseToPhenotypicFeatureAssociation(Association): predicate: Union[str, PredicateType] = None subject: Union[str, DiseaseId] = None object: Union[str, PhenotypicFeatureId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" onset_qualifier: Optional[Union[str, OnsetId]] = None has_count: Optional[int] = None has_total: Optional[int] = None @@ -10374,7 +10374,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class CaseToPhenotypicFeatureAssociation(Association): """ An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or @@ -10391,8 +10391,8 @@ class CaseToPhenotypicFeatureAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -10449,7 +10449,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class BehaviorToBehavioralFeatureAssociation(Association): """ An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has @@ -10466,8 +10466,8 @@ class BehaviorToBehavioralFeatureAssociation(Association): predicate: Union[str, PredicateType] = None subject: Union[str, BehaviorId] = None object: Union[str, BehavioralFeatureId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -10524,7 +10524,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class GeneToEntityAssociationMixin(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] @@ -10556,7 +10556,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class VariantToEntityAssociationMixin(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] @@ -10588,7 +10588,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class GeneToDiseaseOrPhenotypicFeatureAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -10601,8 +10601,8 @@ class GeneToDiseaseOrPhenotypicFeatureAssociation(Association): subject: Union[dict, GeneOrGeneProduct] = None object: Union[str, DiseaseOrPhenotypicFeatureId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" subject_aspect_qualifier: Optional[Union[str, "GeneOrGeneProductOrChemicalEntityAspectEnum"]] = None object_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None frequency_qualifier: Optional[Union[str, FrequencyValue]] = None @@ -10659,7 +10659,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class GeneToPhenotypicFeatureAssociation(GeneToDiseaseOrPhenotypicFeatureAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -10672,8 +10672,8 @@ class GeneToPhenotypicFeatureAssociation(GeneToDiseaseOrPhenotypicFeatureAssocia predicate: Union[str, PredicateType] = None subject: Union[dict, GeneOrGeneProduct] = None object: Union[str, PhenotypicFeatureId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None object_aspect_qualifier: Optional[str] = None @@ -10717,7 +10717,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class GeneToDiseaseAssociation(GeneToDiseaseOrPhenotypicFeatureAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -10730,8 +10730,8 @@ class GeneToDiseaseAssociation(GeneToDiseaseOrPhenotypicFeatureAssociation): predicate: Union[str, PredicateType] = None subject: Union[dict, GeneOrGeneProduct] = None object: Union[str, DiseaseId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None object_aspect_qualifier: Optional[str] = None @@ -10771,7 +10771,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class CausalGeneToDiseaseAssociation(GeneToDiseaseAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -10784,8 +10784,8 @@ class CausalGeneToDiseaseAssociation(GeneToDiseaseAssociation): predicate: Union[str, PredicateType] = None subject: Union[dict, GeneOrGeneProduct] = None object: Union[str, DiseaseId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None object_aspect_qualifier: Optional[str] = None @@ -10825,7 +10825,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class CorrelatedGeneToDiseaseAssociation(GeneToDiseaseAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -10838,8 +10838,8 @@ class CorrelatedGeneToDiseaseAssociation(GeneToDiseaseAssociation): predicate: Union[str, PredicateType] = None subject: Union[dict, GeneOrGeneProduct] = None object: Union[str, DiseaseId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None object_aspect_qualifier: Optional[str] = None @@ -10879,7 +10879,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class DruggableGeneToDiseaseAssociation(GeneToDiseaseAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -10892,8 +10892,8 @@ class DruggableGeneToDiseaseAssociation(GeneToDiseaseAssociation): object: Union[str, DiseaseId] = None subject: Union[dict, GeneOrGeneProduct] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None object_aspect_qualifier: Optional[str] = None @@ -10938,7 +10938,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class PhenotypicFeatureToDiseaseAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -10951,8 +10951,8 @@ class PhenotypicFeatureToDiseaseAssociation(Association): subject: Union[str, NamedThingId] = None object: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -11009,7 +11009,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class VariantToGeneAssociation(Association): """ An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in @@ -11026,8 +11026,8 @@ class VariantToGeneAssociation(Association): subject: Union[str, NamedThingId] = None object: Union[str, GeneId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -11056,7 +11056,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class VariantToGeneExpressionAssociation(VariantToGeneAssociation): """ An association between a variant and expression of a gene (i.e. e-QTL) @@ -11072,8 +11072,8 @@ class VariantToGeneExpressionAssociation(VariantToGeneAssociation): subject: Union[str, NamedThingId] = None object: Union[str, GeneId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" quantifier_qualifier: Optional[Union[str, OntologyClassId]] = None expression_site: Optional[Union[str, AnatomicalEntityId]] = None stage_qualifier: Optional[Union[str, LifeStageId]] = None @@ -11108,7 +11108,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class VariantToPopulationAssociation(Association): """ An association between a variant and a population, where the variant has particular frequency in the population @@ -11124,8 +11124,8 @@ class VariantToPopulationAssociation(Association): predicate: Union[str, PredicateType] = None subject: Union[str, SequenceVariantId] = None object: Union[str, PopulationOfIndividualOrganismsId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" has_quotient: Optional[float] = None has_count: Optional[int] = None has_total: Optional[int] = None @@ -11174,7 +11174,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class PopulationToPopulationAssociation(Association): """ An association between a two populations @@ -11190,8 +11190,8 @@ class PopulationToPopulationAssociation(Association): subject: Union[str, PopulationOfIndividualOrganismsId] = None object: Union[str, PopulationOfIndividualOrganismsId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -11220,7 +11220,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class VariantToPhenotypicFeatureAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -11233,8 +11233,8 @@ class VariantToPhenotypicFeatureAssociation(Association): predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None subject: Union[str, SequenceVariantId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -11291,7 +11291,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class VariantToDiseaseAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -11304,8 +11304,8 @@ class VariantToDiseaseAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -11358,7 +11358,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class GenotypeToDiseaseAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -11371,8 +11371,8 @@ class GenotypeToDiseaseAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -11425,7 +11425,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ModelToDiseaseAssociationMixin(YAMLRoot): """ This mixin is used for any association class for which the subject (source node) plays the role of a 'model', in @@ -11462,7 +11462,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class GeneAsAModelOfDiseaseAssociation(GeneToDiseaseAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -11475,8 +11475,8 @@ class GeneAsAModelOfDiseaseAssociation(GeneToDiseaseAssociation): predicate: Union[str, PredicateType] = None object: Union[str, DiseaseId] = None subject: Union[dict, GeneOrGeneProduct] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None object_aspect_qualifier: Optional[str] = None @@ -11511,7 +11511,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class VariantAsAModelOfDiseaseAssociation(VariantToDiseaseAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -11524,8 +11524,8 @@ class VariantAsAModelOfDiseaseAssociation(VariantToDiseaseAssociation): predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None subject: Union[str, SequenceVariantId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -11568,7 +11568,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class GenotypeAsAModelOfDiseaseAssociation(GenotypeToDiseaseAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -11581,8 +11581,8 @@ class GenotypeAsAModelOfDiseaseAssociation(GenotypeToDiseaseAssociation): predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None subject: Union[str, GenotypeId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -11625,7 +11625,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class CellLineAsAModelOfDiseaseAssociation(CellLineToDiseaseOrPhenotypicFeatureAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -11638,8 +11638,8 @@ class CellLineAsAModelOfDiseaseAssociation(CellLineToDiseaseOrPhenotypicFeatureA predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None subject: Union[str, CellLineId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -11692,7 +11692,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class OrganismalEntityAsAModelOfDiseaseAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -11705,8 +11705,8 @@ class OrganismalEntityAsAModelOfDiseaseAssociation(Association): predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None subject: Union[str, OrganismalEntityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -11759,7 +11759,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class OrganismToOrganismAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -11772,8 +11772,8 @@ class OrganismToOrganismAssociation(Association): predicate: Union[str, PredicateType] = None subject: Union[str, IndividualOrganismId] = None object: Union[str, IndividualOrganismId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -11797,7 +11797,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class TaxonToTaxonAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -11810,8 +11810,8 @@ class TaxonToTaxonAssociation(Association): predicate: Union[str, PredicateType] = None subject: Union[str, OrganismTaxonId] = None object: Union[str, OrganismTaxonId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -11835,7 +11835,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class GeneHasVariantThatContributesToDiseaseAssociation(GeneToDiseaseAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -11848,8 +11848,8 @@ class GeneHasVariantThatContributesToDiseaseAssociation(GeneToDiseaseAssociation subject: Union[dict, GeneOrGeneProduct] = None object: Union[str, DiseaseId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" subject_form_or_variant_qualifier: Optional[str] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -11882,7 +11882,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class GeneToExpressionSiteAssociation(Association): """ An association between a gene and a gene expression site, possibly qualified by stage/timing info. @@ -11898,8 +11898,8 @@ class GeneToExpressionSiteAssociation(Association): subject: Union[dict, GeneOrGeneProduct] = None object: Union[str, AnatomicalEntityId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" stage_qualifier: Optional[Union[str, LifeStageId]] = None quantifier_qualifier: Optional[Union[str, OntologyClassId]] = None @@ -11936,7 +11936,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class SequenceVariantModulatesTreatmentAssociation(Association): """ An association between a sequence variant and a treatment or health intervention. The treatment object itself @@ -11953,8 +11953,8 @@ class SequenceVariantModulatesTreatmentAssociation(Association): predicate: Union[str, PredicateType] = None subject: Union[str, SequenceVariantId] = None object: Union[str, TreatmentId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.subject): @@ -11973,7 +11973,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class FunctionalAssociation(Association): """ An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either @@ -11990,8 +11990,8 @@ class FunctionalAssociation(Association): predicate: Union[str, PredicateType] = None subject: Union[dict, MacromolecularMachineMixin] = None object: Union[str, OntologyClassId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12015,7 +12015,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class MacromolecularMachineToEntityAssociationMixin(YAMLRoot): """ an association which has a macromolecular machine mixin as a subject @@ -12050,7 +12050,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class MacromolecularMachineToMolecularActivityAssociation(FunctionalAssociation): """ A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity @@ -12068,8 +12068,8 @@ class MacromolecularMachineToMolecularActivityAssociation(FunctionalAssociation) predicate: Union[str, PredicateType] = None subject: Union[dict, MacromolecularMachineMixin] = None object: Union[str, MolecularActivityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12093,7 +12093,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class MacromolecularMachineToBiologicalProcessAssociation(FunctionalAssociation): """ A functional association between a macromolecular machine (gene, gene product or complex) and a biological process @@ -12111,8 +12111,8 @@ class MacromolecularMachineToBiologicalProcessAssociation(FunctionalAssociation) predicate: Union[str, PredicateType] = None subject: Union[dict, MacromolecularMachineMixin] = None object: Union[str, BiologicalProcessId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12136,7 +12136,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class MacromolecularMachineToCellularComponentAssociation(FunctionalAssociation): """ A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component @@ -12154,8 +12154,8 @@ class MacromolecularMachineToCellularComponentAssociation(FunctionalAssociation) predicate: Union[str, PredicateType] = None subject: Union[dict, MacromolecularMachineMixin] = None object: Union[str, CellularComponentId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12179,7 +12179,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class MolecularActivityToChemicalEntityAssociation(Association): """ Added in response to capturing relationship between microbiome activities as measured via measurements of blood @@ -12196,8 +12196,8 @@ class MolecularActivityToChemicalEntityAssociation(Association): predicate: Union[str, PredicateType] = None subject: Union[str, MolecularActivityId] = None object: Union[str, ChemicalEntityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12221,7 +12221,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class MolecularActivityToMolecularActivityAssociation(Association): """ Added in response to capturing relationship between microbiome activities as measured via measurements of blood @@ -12238,8 +12238,8 @@ class MolecularActivityToMolecularActivityAssociation(Association): predicate: Union[str, PredicateType] = None subject: Union[str, MolecularActivityId] = None object: Union[str, MolecularActivityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12263,7 +12263,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class GeneToGoTermAssociation(FunctionalAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -12276,8 +12276,8 @@ class GeneToGoTermAssociation(FunctionalAssociation): predicate: Union[str, PredicateType] = None subject: Union[str, GeneId] = None object: Union[str, OntologyClassId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12301,7 +12301,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class EntityToDiseaseAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -12314,8 +12314,8 @@ class EntityToDiseaseAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" clinical_approval_status: Optional[Union[str, "ClinicalApprovalStatusEnum"]] = None max_research_phase: Optional[Union[str, "MaxResearchPhaseEnum"]] = None @@ -12337,7 +12337,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class EntityToPhenotypicFeatureAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -12350,8 +12350,8 @@ class EntityToPhenotypicFeatureAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" clinical_approval_status: Optional[Union[str, "ClinicalApprovalStatusEnum"]] = None max_research_phase: Optional[Union[str, "MaxResearchPhaseEnum"]] = None @@ -12373,7 +12373,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class SequenceAssociation(Association): """ An association between a sequence feature and a nucleic acid entity it is localized to. @@ -12389,8 +12389,8 @@ class SequenceAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12404,7 +12404,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class GenomicSequenceLocalization(SequenceAssociation): """ A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may @@ -12421,8 +12421,8 @@ class GenomicSequenceLocalization(SequenceAssociation): subject: Union[str, NucleicAcidEntityId] = None object: Union[str, NucleicAcidEntityId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" start_interbase_coordinate: Optional[int] = None end_interbase_coordinate: Optional[int] = None genome_build: Optional[Union[str, "StrandEnum"]] = None @@ -12471,7 +12471,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class SequenceFeatureRelationship(Association): """ For example, a particular exon is part of a particular transcript or gene @@ -12487,8 +12487,8 @@ class SequenceFeatureRelationship(Association): predicate: Union[str, PredicateType] = None subject: Union[str, NucleicAcidEntityId] = None object: Union[str, NucleicAcidEntityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12512,7 +12512,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class TranscriptToGeneRelationship(SequenceFeatureRelationship): """ A gene is a collection of transcripts @@ -12528,8 +12528,8 @@ class TranscriptToGeneRelationship(SequenceFeatureRelationship): predicate: Union[str, PredicateType] = None subject: Union[str, TranscriptId] = None object: Union[str, GeneId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12553,7 +12553,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class GeneToGeneProductRelationship(SequenceFeatureRelationship): """ A gene is transcribed and potentially translated to a gene product @@ -12569,8 +12569,8 @@ class GeneToGeneProductRelationship(SequenceFeatureRelationship): subject: Union[str, GeneId] = None object: Union[dict, GeneProductMixin] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12599,7 +12599,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ExonToTranscriptRelationship(SequenceFeatureRelationship): """ A transcript is formed from multiple exons @@ -12615,8 +12615,8 @@ class ExonToTranscriptRelationship(SequenceFeatureRelationship): predicate: Union[str, PredicateType] = None subject: Union[str, ExonId] = None object: Union[str, TranscriptId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12640,7 +12640,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation(Association): """ A regulatory relationship between two genes @@ -12656,8 +12656,8 @@ class ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation(Association): predicate: Union[str, PredicateType] = None subject: Union[dict, ChemicalEntityOrGeneOrGeneProduct] = None object: Union[dict, GeneOrGeneProduct] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" object_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -12690,7 +12690,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class AnatomicalEntityToAnatomicalEntityAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -12703,8 +12703,8 @@ class AnatomicalEntityToAnatomicalEntityAssociation(Association): predicate: Union[str, PredicateType] = None subject: Union[str, AnatomicalEntityId] = None object: Union[str, AnatomicalEntityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.subject): @@ -12723,7 +12723,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class AnatomicalEntityToAnatomicalEntityPartOfAssociation(AnatomicalEntityToAnatomicalEntityAssociation): """ A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are @@ -12741,8 +12741,8 @@ class AnatomicalEntityToAnatomicalEntityPartOfAssociation(AnatomicalEntityToAnat subject: Union[str, AnatomicalEntityId] = None object: Union[str, AnatomicalEntityId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12771,7 +12771,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class AnatomicalEntityToAnatomicalEntityOntogenicAssociation(AnatomicalEntityToAnatomicalEntityAssociation): """ A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are @@ -12789,8 +12789,8 @@ class AnatomicalEntityToAnatomicalEntityOntogenicAssociation(AnatomicalEntityToA subject: Union[str, AnatomicalEntityId] = None object: Union[str, AnatomicalEntityId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12819,7 +12819,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class OrganismTaxonToEntityAssociation(YAMLRoot): """ An association between an organism taxon and another entity @@ -12854,7 +12854,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class OrganismTaxonToOrganismTaxonAssociation(Association): """ A relationship between two organism taxon nodes @@ -12870,8 +12870,8 @@ class OrganismTaxonToOrganismTaxonAssociation(Association): predicate: Union[str, PredicateType] = None subject: Union[str, OrganismTaxonId] = None object: Union[str, OrganismTaxonId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.predicate): @@ -12895,7 +12895,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class OrganismTaxonToOrganismTaxonSpecialization(OrganismTaxonToOrganismTaxonAssociation): """ A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo @@ -12911,8 +12911,8 @@ class OrganismTaxonToOrganismTaxonSpecialization(OrganismTaxonToOrganismTaxonAss subject: Union[str, OrganismTaxonId] = None object: Union[str, OrganismTaxonId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12941,7 +12941,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class OrganismTaxonToOrganismTaxonInteraction(OrganismTaxonToOrganismTaxonAssociation): """ An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and @@ -12959,8 +12959,8 @@ class OrganismTaxonToOrganismTaxonInteraction(OrganismTaxonToOrganismTaxonAssoci subject: Union[str, OrganismTaxonId] = None object: Union[str, OrganismTaxonId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" associated_environmental_context: Optional[str] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -12993,7 +12993,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass(repr=False) +@dataclass class OrganismTaxonToEnvironmentAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -13006,8 +13006,8 @@ class OrganismTaxonToEnvironmentAssociation(Association): subject: Union[str, OrganismTaxonId] = None object: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = KnowledgeLevelEnum.not_provided - agent_type: Union[str, "AgentTypeEnum"] = AgentTypeEnum.not_provided + knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" + agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.subject): diff --git a/src/biolink_model/datamodel/pydanticmodel_v2.py b/src/biolink_model/datamodel/pydanticmodel_v2.py index 292a514cb..6c1905bd0 100644 --- a/src/biolink_model/datamodel/pydanticmodel_v2.py +++ b/src/biolink_model/datamodel/pydanticmodel_v2.py @@ -1 +1 @@ -gen-pydantic, version 1.8.3 +gen-pydantic, version 1.7.8 diff --git a/src/biolink_model/scripts/classprefixes.py b/src/biolink_model/scripts/classprefixes.py index 2392b3490..ac1d165af 100644 --- a/src/biolink_model/scripts/classprefixes.py +++ b/src/biolink_model/scripts/classprefixes.py @@ -1,5 +1,5 @@ # Auto generated from class_prefixes.yaml by pythongen.py version: 0.0.1 -# Generation date: 2024-09-23T16:45:40 +# Generation date: 2024-09-23T23:51:59 # Schema: BiolinkClassPrefixes # # id: biolink-model-class-prefixes @@ -11,7 +11,7 @@ from jsonasobj2 import JsonObj, as_dict from typing import Optional, List, Union, Dict, ClassVar, Any from dataclasses import dataclass -from datetime import date, datetime, time +from datetime import date, datetime from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions from linkml_runtime.utils.slot import Slot @@ -50,7 +50,7 @@ -@dataclass(repr=False) +@dataclass class BiolinkClassPrefixMap(YAMLRoot): """ preferred order identifier prefixes per class in Biolink Model @@ -76,7 +76,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class BiolinkClassPrefixesCollection(YAMLRoot): """ collection of BiolinkClassPrefixes objects @@ -98,7 +98,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass(repr=False) +@dataclass class Prefix(YAMLRoot): _inherited_slots: ClassVar[List[str]] = []