diff --git a/erdiagram-autogen/kbmodel.md b/erdiagram-autogen/kbmodel.md index 60afce2b..a1da6f22 100644 --- a/erdiagram-autogen/kbmodel.md +++ b/erdiagram-autogen/kbmodel.md @@ -1,25 +1,324 @@ ```mermaid erDiagram +LibraryPool { + integer avg_size_bp + float tube_contents + string id + iri_type iri + category_typeList category + stringList type + label_type name + narrative_text description +} +Agent { + uriorcurieList affiliation + string address + stringList provided_by + uriorcurieList xref + label_type full_name + label_typeList synonym + string id + iri_type iri + category_typeList category + stringList type + label_type name + narrative_text description +} +LibraryPooling { + stringList provided_by + uriorcurieList xref + label_type full_name + label_typeList synonym + string id + iri_type iri + category_typeList category + stringList type + label_type name + narrative_text description +} +LibraryAliquot { + integer input_quantity + string id + iri_type iri + category_typeList category + stringList type + label_type name + narrative_text description +} +LibraryAliquoting { + stringList provided_by + uriorcurieList xref + label_type full_name + label_typeList synonym + string id + iri_type iri + category_typeList category + stringList type + label_type name + narrative_text description +} +Library { + string method + datetime creation_date + float input_quantity + boolean process_pass + integer avg_size_bp + float quantification_fmol + float quantification_ng + float quantification_nm + string r1_index + string r1_sequence + string r2_index + string r2_sequence + string id + iri_type iri + category_typeList category + stringList type + label_type name + narrative_text description +} +LibraryConstruction { + stringList provided_by + uriorcurieList xref + label_type full_name + label_typeList synonym + string id + iri_type iri + category_typeList category + stringList type + label_type name + narrative_text description +} +AmplifiedCdna { + string method + float input_quantity + boolean process_pass + integer pcr_cycles + float percent_cdna_longer_than_400bp + string id + iri_type iri + category_typeList category + stringList type + label_type name + narrative_text description +} +CdnaAmplification { + stringList provided_by + uriorcurieList xref + label_type full_name + label_typeList synonym + string id + iri_type iri + category_typeList category + stringList type + label_type name + narrative_text description +} +BarcodedCellSample { + string port_well + string sample_quality_count + string id + iri_type iri + category_typeList category + stringList type + label_type name + narrative_text description +} +CellBarcoding { + stringList provided_by + uriorcurieList xref + label_type full_name + label_typeList synonym + string id + iri_type iri + category_typeList category + stringList type + label_type name + narrative_text description +} +EnrichedCellSample { + string id + iri_type iri + category_typeList category + stringList type + label_type name + narrative_text description +} +CellEnrichment { + stringList provided_by + uriorcurieList xref + label_type full_name + label_typeList synonym + string id + iri_type iri + category_typeList category + stringList type + label_type name + narrative_text description +} +DissociatedCellSample { + string cell_prep_type + string facs_population_plan + integer num_cells_collected + string id + iri_type iri + category_typeList category + stringList type + label_type name + narrative_text description +} +CellDissociation { + stringList provided_by + uriorcurieList xref + label_type full_name + label_typeList synonym + string id + iri_type iri + category_typeList category + stringList type + label_type name + narrative_text description +} +TissueSample { + string roi_plan + string roi_label + string id + iri_type iri + category_typeList category + stringList type + label_type name + narrative_text description +} +TissueDissecting { + stringList provided_by + uriorcurieList xref + label_type full_name + label_typeList synonym + string id + iri_type iri + category_typeList category + stringList type + label_type name + narrative_text description +} +BrainSection { + integer ordinal + string id + iri_type iri + category_typeList category + stringList type + label_type name + narrative_text description +} +BrainSegmentSectioning { + stringList provided_by + uriorcurieList xref + label_type full_name + label_typeList synonym + string id + iri_type iri + category_typeList category + stringList type + label_type name + narrative_text description +} +BrainSegment { + string anatomical_division + string id + iri_type iri + category_typeList category + stringList type + label_type name + narrative_text description +} +BrainExtraction { + stringList provided_by + uriorcurieList xref + label_type full_name + label_typeList synonym + string id + iri_type iri + category_typeList category + stringList type + label_type name + narrative_text description +} +Donor { + SexType sex + date birth_date + date death_date + string death_age + string full_genotype + label_type in_taxon_label + uriorcurieList affiliation + string address + stringList provided_by + uriorcurieList xref + label_type full_name + label_typeList synonym + string id + iri_type iri + category_typeList category + stringList type + label_type name + narrative_text description +} +ProvEntity { + +} +Activity { + stringList provided_by + uriorcurieList xref + label_type full_name + label_typeList synonym + string id + iri_type iri + category_typeList category + stringList type + label_type name + narrative_text description +} +Entity { + string id + iri_type iri + category_typeList category + stringList type + label_type name + narrative_text description +} +ProvActivity { + +} AnnotationCollection { } GenomeAssembly { - string id - string taxon string version - string label - string description + string strain + label_type in_taxon_label + stringList provided_by + uriorcurieList xref + label_type full_name + label_typeList synonym + string id + iri_type iri + category_typeList category + stringList type + label_type name + narrative_text description } GenomeAnnotation { uriorcurie reference_assembly string version stringList content_url + string authority biological_sequence has_biological_sequence string id label_type in_taxon_label stringList provided_by uriorcurieList xref label_type full_name + label_typeList synonym iri_type iri category_typeList category stringList type @@ -30,28 +329,19 @@ GeneAnnotation { BioType molecular_type string source_id string symbol - label_typeList synonym uriorcurieList xref biological_sequence has_biological_sequence string id label_type in_taxon_label stringList provided_by label_type full_name + label_typeList synonym iri_type iri category_typeList category stringList type symbol_type name narrative_text description } -Mappings { - -} -Mapping { - string authority - string method - string creation_date - string access_date -} Checksum { DigestType checksum_algorithm string value @@ -63,19 +353,108 @@ Checksum { narrative_text description } +LibraryPool ||--}o LibraryAliquot : "wasDerivedFrom" +LibraryPool ||--}o LibraryPooling : "wasGeneratedBy" +LibraryPool ||--}o Agent : "wasAttributedTo" +LibraryPool ||--}o Attribute : "has attribute" +Agent ||--}o Attribute : "has attribute" +LibraryPooling ||--}o LibraryAliquot : "used" +LibraryPooling ||--}o LibraryPool : "generated" +LibraryPooling ||--}o Agent : "wasAssociatedWith" +LibraryPooling ||--}o Attribute : "has attribute" +LibraryAliquot ||--}o Library : "wasDerivedFrom" +LibraryAliquot ||--}o LibraryAliquoting : "wasGeneratedBy" +LibraryAliquot ||--}o Agent : "wasAttributedTo" +LibraryAliquot ||--}o Attribute : "has attribute" +LibraryAliquoting ||--}o Library : "used" +LibraryAliquoting ||--}o LibraryAliquot : "generated" +LibraryAliquoting ||--}o Agent : "wasAssociatedWith" +LibraryAliquoting ||--}o Attribute : "has attribute" +Library ||--}o AmplifiedCdna : "wasDerivedFrom" +Library ||--}o LibraryConstruction : "wasGeneratedBy" +Library ||--}o Agent : "wasAttributedTo" +Library ||--}o Attribute : "has attribute" +LibraryConstruction ||--}o AmplifiedCdna : "used" +LibraryConstruction ||--}o Library : "generated" +LibraryConstruction ||--}o Agent : "wasAssociatedWith" +LibraryConstruction ||--}o Attribute : "has attribute" +AmplifiedCdna ||--}o BarcodedCellSample : "wasDerivedFrom" +AmplifiedCdna ||--}o CdnaAmplification : "wasGeneratedBy" +AmplifiedCdna ||--}o Agent : "wasAttributedTo" +AmplifiedCdna ||--}o Attribute : "has attribute" +CdnaAmplification ||--}o BarcodedCellSample : "used" +CdnaAmplification ||--}o AmplifiedCdna : "generated" +CdnaAmplification ||--}o Agent : "wasAssociatedWith" +CdnaAmplification ||--}o Attribute : "has attribute" +BarcodedCellSample ||--}o EnrichedCellSample : "wasDerivedFrom" +BarcodedCellSample ||--}o CellBarcoding : "wasGeneratedBy" +BarcodedCellSample ||--}o Agent : "wasAttributedTo" +BarcodedCellSample ||--}o Attribute : "has attribute" +CellBarcoding ||--}o EnrichedCellSample : "used" +CellBarcoding ||--}o BarcodedCellSample : "generated" +CellBarcoding ||--}o Agent : "wasAssociatedWith" +CellBarcoding ||--}o Attribute : "has attribute" +EnrichedCellSample ||--}o DissociatedCellSample : "wasDerivedFrom" +EnrichedCellSample ||--}o CellEnrichment : "wasGeneratedBy" +EnrichedCellSample ||--}o Agent : "wasAttributedTo" +EnrichedCellSample ||--}o Attribute : "has attribute" +CellEnrichment ||--}o DissociatedCellSample : "used" +CellEnrichment ||--}o EnrichedCellSample : "generated" +CellEnrichment ||--}o Agent : "wasAssociatedWith" +CellEnrichment ||--}o Attribute : "has attribute" +DissociatedCellSample ||--}o TissueSample : "wasDerivedFrom" +DissociatedCellSample ||--}o CellDissociation : "wasGeneratedBy" +DissociatedCellSample ||--}o Agent : "wasAttributedTo" +DissociatedCellSample ||--}o Attribute : "has attribute" +CellDissociation ||--}o TissueSample : "used" +CellDissociation ||--}o DissociatedCellSample : "generated" +CellDissociation ||--}o Agent : "wasAssociatedWith" +CellDissociation ||--}o Attribute : "has attribute" +TissueSample ||--}o BrainSection : "wasDerivedFrom" +TissueSample ||--}o TissueDissecting : "wasGeneratedBy" +TissueSample ||--}o Agent : "wasAttributedTo" +TissueSample ||--}o Attribute : "has attribute" +TissueDissecting ||--}o BrainSection : "used" +TissueDissecting ||--}o TissueSample : "generated" +TissueDissecting ||--}o Agent : "wasAssociatedWith" +TissueDissecting ||--}o Attribute : "has attribute" +BrainSection ||--}o BrainSegment : "wasDerivedFrom" +BrainSection ||--}o BrainSegmentSectioning : "wasGeneratedBy" +BrainSection ||--}o Agent : "wasAttributedTo" +BrainSection ||--}o Attribute : "has attribute" +BrainSegmentSectioning ||--}o BrainSegment : "used" +BrainSegmentSectioning ||--}o BrainSection : "generated" +BrainSegmentSectioning ||--}o Agent : "wasAssociatedWith" +BrainSegmentSectioning ||--}o Attribute : "has attribute" +BrainSegment ||--}o Donor : "wasDerivedFrom" +BrainSegment ||--}o BrainExtraction : "wasGeneratedBy" +BrainSegment ||--}o Agent : "wasAttributedTo" +BrainSegment ||--}o Attribute : "has attribute" +BrainExtraction ||--}o Donor : "used" +BrainExtraction ||--}o BrainSegment : "generated" +BrainExtraction ||--}o Agent : "wasAssociatedWith" +BrainExtraction ||--}o Attribute : "has attribute" +Donor ||--}o OrganismTaxon : "in taxon" +Donor ||--}o Attribute : "has attribute" +ProvEntity ||--}o Entity : "wasDerivedFrom" +ProvEntity ||--}o Activity : "wasGeneratedBy" +ProvEntity ||--}o Agent : "wasAttributedTo" +Activity ||--}o Attribute : "has attribute" +Entity ||--}o Attribute : "has attribute" +ProvActivity ||--}o Entity : "used" +ProvActivity ||--}o Entity : "generated" +ProvActivity ||--}o Agent : "wasAssociatedWith" AnnotationCollection ||--}o GeneAnnotation : "annotations" AnnotationCollection ||--}o GenomeAnnotation : "genome_annotations" AnnotationCollection ||--}o GenomeAssembly : "genome_assemblies" +GenomeAssembly ||--}o OrganismTaxon : "in taxon" +GenomeAssembly ||--}o Attribute : "has attribute" GenomeAnnotation ||--}| Checksum : "digest" GenomeAnnotation ||--}o OrganismTaxon : "in taxon" GenomeAnnotation ||--}o Attribute : "has attribute" GeneAnnotation ||--|o GenomeAnnotation : "referenced in" GeneAnnotation ||--}o OrganismTaxon : "in taxon" GeneAnnotation ||--}o Attribute : "has attribute" -Mappings ||--}o NamedThing : "has member" -Mapping ||--|o GeneAnnotation : "gene_identifier_1" -Mapping ||--|o GeneAnnotation : "gene_identifier_2" -Mapping ||--}o NamedThing : "member of" Checksum ||--}o Attribute : "has attribute" ``` diff --git a/json-schema-autogen/kbmodel.json b/json-schema-autogen/kbmodel.json index 0b9cd835..13808c61 100644 --- a/json-schema-autogen/kbmodel.json +++ b/json-schema-autogen/kbmodel.json @@ -61,6 +61,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -128,6 +135,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -206,6 +220,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -227,6 +248,90 @@ "title": "Agent", "type": "object" }, + "AmplifiedCdna": { + "additionalProperties": false, + "description": "", + "properties": { + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "input_quantity": { + "description": "The amount of input cDNA (ng) amplified.", + "type": "number" + }, + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "type": "string" + }, + "method": { + "type": "string" + }, + "name": { + "description": "A human-readable name for an attribute or entity.", + "type": "string" + }, + "pcr_cycles": { + "description": "Number of PCR cycles used to amplify the cDNA.", + "type": "integer" + }, + "percent_cdna_longer_than_400bp": { + "description": "The percentage of cDNA fragments that are longer than 400bp.", + "type": "number" + }, + "process_pass": { + "description": "Indicates whether the rna amplification process passed or failed.", + "type": "boolean" + }, + "type": { + "items": { + "type": "string" + }, + "type": "array" + }, + "wasAttributedTo": { + "items": { + "$ref": "#/$defs/Agent" + }, + "type": "array" + }, + "wasDerivedFrom": { + "items": { + "$ref": "#/$defs/BarcodedCellSample" + }, + "type": "array" + }, + "wasGeneratedBy": { + "items": { + "$ref": "#/$defs/CdnaAmplification" + }, + "type": "array" + } + }, + "required": [ + "id" + ], + "title": "AmplifiedCdna", + "type": "object" + }, "AnatomicalEntity": { "additionalProperties": false, "description": "A subcellular location, cell type or gross anatomical part", @@ -284,6 +389,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -805,6 +917,13 @@ "description": "executive summary of a publication", "type": "string" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -1077,6 +1196,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -1156,6 +1282,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -1177,6 +1310,77 @@ "title": "Bacterium", "type": "object" }, + "BarcodedCellSample": { + "additionalProperties": false, + "description": "", + "properties": { + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "type": "string" + }, + "name": { + "description": "A human-readable name for an attribute or entity.", + "type": "string" + }, + "port_well": { + "type": "string" + }, + "sample_quality_count": { + "type": "string" + }, + "type": { + "items": { + "type": "string" + }, + "type": "array" + }, + "wasAttributedTo": { + "items": { + "$ref": "#/$defs/Agent" + }, + "type": "array" + }, + "wasDerivedFrom": { + "items": { + "$ref": "#/$defs/EnrichedCellSample" + }, + "type": "array" + }, + "wasGeneratedBy": { + "items": { + "$ref": "#/$defs/CellBarcoding" + }, + "type": "array" + } + }, + "required": [ + "id" + ], + "title": "BarcodedCellSample", + "type": "object" + }, "Behavior": { "additionalProperties": false, "description": "", @@ -1255,6 +1459,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -1553,6 +1764,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "timepoint": { "description": "a point in time", "format": "time", @@ -1637,6 +1855,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -1751,6 +1976,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -1850,6 +2082,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -1932,6 +2171,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -2015,6 +2261,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "timepoint": { "description": "a point in time", "format": "time", @@ -2134,6 +2387,13 @@ "description": "executive summary of a publication", "type": "string" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "description": "Should generally be set to an ontology class defined term for 'book'.", "items": { @@ -2256,6 +2516,13 @@ "description": "executive summary of a publication", "type": "string" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -2282,9 +2549,9 @@ "title": "BookChapter", "type": "object" }, - "Case": { + "BrainExtraction": { "additionalProperties": false, - "description": "An individual (human) organism that has a patient role in some clinical context.", + "description": "A process that takes a brain sample from a donor and produces a brain segment.", "properties": { "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -2302,8 +2569,14 @@ "description": "a long-form human readable name for a thing", "type": "string" }, + "generated": { + "items": { + "$ref": "#/$defs/BrainSegment" + }, + "type": "array" + }, "has_attribute": { - "description": "may often be an organism attribute", + "description": "connects any entity to an attribute", "items": { "type": "string" }, @@ -2313,17 +2586,6 @@ "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, - "in_taxon": { - "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", - "items": { - "type": "string" - }, - "type": "array" - }, - "in_taxon_label": { - "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" - }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" @@ -2339,12 +2601,31 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" }, "type": "array" }, + "used": { + "items": { + "$ref": "#/$defs/Donor" + }, + "type": "array" + }, + "wasAssociatedWith": { + "items": { + "$ref": "#/$defs/Agent" + }, + "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": { @@ -2357,20 +2638,13 @@ "id", "category" ], - "title": "Case", + "title": "BrainExtraction", "type": "object" }, - "CaseToPhenotypicFeatureAssociation": { + "BrainSection": { "additionalProperties": false, - "description": "An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype.", + "description": "", "properties": { - "aggregator_knowledge_source": { - "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", - "items": { - "type": "string" - }, - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { @@ -2382,10 +2656,6 @@ "description": "a human-readable description of an entity", "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" - }, "has_attribute": { "description": "connects any entity to an attribute", "items": { @@ -2393,28 +2663,6 @@ }, "type": "array" }, - "has_count": { - "description": "number of things with a particular property", - "type": "integer" - }, - "has_evidence": { - "description": "connects an association to an instance of supporting evidence", - "items": { - "type": "string" - }, - "type": "array" - }, - "has_percentage": { - "description": "equivalent to has quotient multiplied by 100", - "type": "number" - }, - "has_quotient": { - "type": "number" - }, - "has_total": { - "description": "total number of things in a particular reference set", - "type": "integer" - }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" @@ -2423,173 +2671,121 @@ "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "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" - }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" }, - "negated": { - "description": "if set to true, then the association is negated i.e. is not true", - "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.", - "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" + "ordinal": { + "description": "The ordinal number of the section.", + "type": "integer" }, - "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.", + "type": { "items": { "type": "string" }, "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.", + "wasAttributedTo": { "items": { - "type": "string" + "$ref": "#/$defs/Agent" }, "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.", + "wasDerivedFrom": { "items": { - "type": "string" + "$ref": "#/$defs/BrainSegment" }, "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" - }, - "onset_qualifier": { - "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", - "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" - }, - "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" - }, - "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" - }, - "predicate": { - "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", - "type": "string" - }, - "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" - }, - "publications": { - "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", + "wasGeneratedBy": { "items": { - "type": "string" + "$ref": "#/$defs/BrainSegmentSectioning" }, "type": "array" + } + }, + "required": [ + "id" + ], + "title": "BrainSection", + "type": "object" + }, + "BrainSegment": { + "additionalProperties": false, + "description": "", + "properties": { + "anatomical_division": { + "type": "string" }, - "qualifiers": { - "description": "connects an association to qualifiers that modify or qualify the meaning of that association", + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { "type": "string" }, "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.", + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", "items": { "type": "string" }, "type": "array" }, - "severity_qualifier": { - "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", - "type": "string" - }, - "sex_qualifier": { - "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, - "subject": { - "description": "the case (e.g. patient) that has the property", + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", "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.", + "name": { + "description": "A human-readable name for an attribute or entity.", "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.", + "type": { "items": { "type": "string" }, "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.", + "wasAttributedTo": { "items": { - "type": "string" + "$ref": "#/$defs/Agent" }, "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.", + "wasDerivedFrom": { "items": { - "type": "string" + "$ref": "#/$defs/Donor" }, "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" - }, - "timepoint": { - "description": "a point in time", - "format": "time", - "type": "string" - }, - "type": { - "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", + "wasGeneratedBy": { "items": { - "type": "string" + "$ref": "#/$defs/BrainExtraction" }, "type": "array" } }, "required": [ - "subject", - "predicate", - "object", "id" ], - "title": "CaseToPhenotypicFeatureAssociation", + "title": "BrainSegment", "type": "object" }, - "CausalGeneToDiseaseAssociation": { + "BrainSegmentSectioning": { "additionalProperties": false, - "description": "", + "description": "A process that takes a brain segment and produces a brain section.", "properties": { - "aggregator_knowledge_source": { - "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", - "items": { - "type": "string" - }, - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" @@ -2598,39 +2794,23 @@ "description": "a human-readable description of an entity", "type": "string" }, - "frequency_qualifier": { - "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", + "full_name": { + "description": "a long-form human readable name for a thing", "type": "string" }, - "has_attribute": { - "description": "connects any entity to an attribute", + "generated": { "items": { - "type": "string" + "$ref": "#/$defs/BrainSection" }, "type": "array" }, - "has_count": { - "description": "number of things with a particular property", - "type": "integer" - }, - "has_evidence": { - "description": "connects an association to an instance of supporting evidence", + "has_attribute": { + "description": "connects any entity to an attribute", "items": { "type": "string" }, "type": "array" }, - "has_percentage": { - "description": "equivalent to has quotient multiplied by 100", - "type": "number" - }, - "has_quotient": { - "type": "number" - }, - "has_total": { - "description": "total number of things in a particular reference set", - "type": "integer" - }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" @@ -2639,150 +2819,44 @@ "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "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" - }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" }, - "negated": { - "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" - }, - "object": { - "description": "disease", - "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" - }, - "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.", + "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" }, - "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.", + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, "type": "array" }, - "object_direction_qualifier": { - "$ref": "#/$defs/DirectionQualifierEnum" - }, - "object_label_closure": { - "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", + "type": { "items": { "type": "string" }, "type": "array" }, - "object_namespace": { - "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "used": { + "items": { + "$ref": "#/$defs/BrainSegment" + }, + "type": "array" }, - "onset_qualifier": { - "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", - "type": "string" + "wasAssociatedWith": { + "items": { + "$ref": "#/$defs/Agent" + }, + "type": "array" }, - "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" - }, - "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" - }, - "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" - }, - "predicate": { - "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", - "type": "string" - }, - "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" - }, - "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" - }, - "qualifiers": { - "description": "connects an association to qualifiers that modify or qualify the meaning of that association", - "items": { - "type": "string" - }, - "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" - }, - "severity_qualifier": { - "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", - "type": "string" - }, - "sex_qualifier": { - "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" - }, - "subject": { - "$ref": "#/$defs/GeneOrGeneProduct", - "description": "gene in which variation is shown to cause the disease." - }, - "subject_aspect_qualifier": { - "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum" - }, - "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" - }, - "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" - }, - "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" - }, - "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" - }, - "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" - }, - "timepoint": { - "description": "a point in time", - "format": "time", - "type": "string" - }, - "type": { - "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", + "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" }, @@ -2790,42 +2864,15 @@ } }, "required": [ - "subject", - "predicate", - "object", - "id" + "id", + "category" ], - "title": "CausalGeneToDiseaseAssociation", + "title": "BrainSegmentSectioning", "type": "object" }, - "CausalMechanismQualifierEnum": { - "description": "", - "enum": [ - "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" - ], - "title": "CausalMechanismQualifierEnum", - "type": "string" - }, - "Cell": { + "Case": { "additionalProperties": false, - "description": "", + "description": "An individual (human) organism that has a patient role in some clinical context.", "properties": { "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -2880,79 +2927,8 @@ }, "type": "array" }, - "type": { - "items": { - "type": "string" - }, - "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" - } - }, - "required": [ - "id", - "category" - ], - "title": "Cell", - "type": "object" - }, - "CellLine": { - "additionalProperties": false, - "description": "", - "properties": { - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", - "items": { - "pattern": "^biolink:[A-Z][A-Za-z]+$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of an entity", - "type": "string" - }, - "full_name": { - "description": "a long-form human readable name for a thing", - "type": "string" - }, - "has_attribute": { - "description": "may often be an organism attribute", - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", - "type": "string" - }, - "in_taxon": { - "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", - "items": { - "type": "string" - }, - "type": "array" - }, - "in_taxon_label": { - "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" - }, - "iri": { - "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" - }, - "name": { - "description": "A human-readable name for an attribute or entity.", - "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.", + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, @@ -2976,12 +2952,12 @@ "id", "category" ], - "title": "CellLine", + "title": "Case", "type": "object" }, - "CellLineAsAModelOfDiseaseAssociation": { + "CaseToPhenotypicFeatureAssociation": { "additionalProperties": false, - "description": "", + "description": "An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype.", "properties": { "aggregator_knowledge_source": { "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", @@ -3012,6 +2988,10 @@ }, "type": "array" }, + "has_count": { + "description": "number of things with a particular property", + "type": "integer" + }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { @@ -3019,6 +2999,17 @@ }, "type": "array" }, + "has_percentage": { + "description": "equivalent to has quotient multiplied by 100", + "type": "number" + }, + "has_quotient": { + "type": "number" + }, + "has_total": { + "description": "total number of things in a particular reference set", + "type": "integer" + }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" @@ -3040,7 +3031,7 @@ "type": "boolean" }, "object": { - "description": "disease", + "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string" }, "object_category": { @@ -3089,7 +3080,7 @@ "type": "string" }, "predicate": { - "description": "The relationship to the disease", + "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string" }, "primary_knowledge_source": { @@ -3121,8 +3112,12 @@ "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string" }, + "sex_qualifier": { + "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", + "type": "string" + }, "subject": { - "description": "A cell line derived from an organismal entity with a disease state that is used as a model of that disease.", + "description": "the case (e.g. patient) that has the property", "type": "string" }, "subject_category": { @@ -3173,12 +3168,12 @@ "object", "id" ], - "title": "CellLineAsAModelOfDiseaseAssociation", + "title": "CaseToPhenotypicFeatureAssociation", "type": "object" }, - "CellLineToDiseaseOrPhenotypicFeatureAssociation": { + "CausalGeneToDiseaseAssociation": { "additionalProperties": false, - "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.", + "description": "", "properties": { "aggregator_knowledge_source": { "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", @@ -3198,6 +3193,10 @@ "description": "a human-readable description of an entity", "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" + }, "has_attribute": { "description": "connects any entity to an attribute", "items": { @@ -3205,6 +3204,10 @@ }, "type": "array" }, + "has_count": { + "description": "number of things with a particular property", + "type": "integer" + }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { @@ -3212,12 +3215,23 @@ }, "type": "array" }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", - "type": "string" + "has_percentage": { + "description": "equivalent to has quotient multiplied by 100", + "type": "number" }, - "iri": { - "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "has_quotient": { + "type": "number" + }, + "has_total": { + "description": "total number of things in a particular reference set", + "type": "integer" + }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, "knowledge_source": { @@ -3233,7 +3247,7 @@ "type": "boolean" }, "object": { - "description": "disease or phenotype", + "description": "disease", "type": "string" }, "object_category": { @@ -3254,6 +3268,9 @@ }, "type": "array" }, + "object_direction_qualifier": { + "$ref": "#/$defs/DirectionQualifierEnum" + }, "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": { @@ -3265,6 +3282,10 @@ "description": "Used to 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" }, + "onset_qualifier": { + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "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" @@ -3306,10 +3327,21 @@ }, "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.", + "severity_qualifier": { + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "type": "string" + }, + "sex_qualifier": { + "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string" }, + "subject": { + "$ref": "#/$defs/GeneOrGeneProduct", + "description": "gene in which variation is shown to cause the disease." + }, + "subject_aspect_qualifier": { + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum" + }, "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" @@ -3358,12 +3390,37 @@ "object", "id" ], - "title": "CellLineToDiseaseOrPhenotypicFeatureAssociation", + "title": "CausalGeneToDiseaseAssociation", "type": "object" }, - "CellularComponent": { + "CausalMechanismQualifierEnum": { + "description": "", + "enum": [ + "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" + ], + "title": "CausalMechanismQualifierEnum", + "type": "string" + }, + "CdnaAmplification": { "additionalProperties": false, - "description": "A location in or around a cell", + "description": "A process that takes a barcoded cell sample and produces an amplified cDNA sample.", "properties": { "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -3381,26 +3438,21 @@ "description": "a long-form human readable name for a thing", "type": "string" }, - "has_attribute": { - "description": "may often be an organism attribute", + "generated": { "items": { - "type": "string" + "$ref": "#/$defs/AmplifiedCdna" }, "type": "array" }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", - "type": "string" - }, - "in_taxon": { - "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", + "has_attribute": { + "description": "connects any entity to an attribute", "items": { "type": "string" }, "type": "array" }, - "in_taxon_label": { - "description": "The human readable scientific name for the taxon of the entity.", + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, "iri": { @@ -3418,12 +3470,31 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" }, "type": "array" }, + "used": { + "items": { + "$ref": "#/$defs/BarcodedCellSample" + }, + "type": "array" + }, + "wasAssociatedWith": { + "items": { + "$ref": "#/$defs/Agent" + }, + "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": { @@ -3436,10 +3507,10 @@ "id", "category" ], - "title": "CellularComponent", + "title": "CdnaAmplification", "type": "object" }, - "CellularOrganism": { + "Cell": { "additionalProperties": false, "description": "", "properties": { @@ -3496,6 +3567,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -3514,27 +3592,35 @@ "id", "category" ], - "title": "CellularOrganism", + "title": "Cell", "type": "object" }, - "Checksum": { + "CellBarcoding": { "additionalProperties": false, - "description": "Checksum values associated with digital entities.", + "description": "A process that takes an enriched cell sample and produces a barcoded cell sample.", "properties": { "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" }, - "checksum_algorithm": { - "$ref": "#/$defs/DigestType" - }, "description": { "description": "a human-readable description of an entity", "type": "string" }, + "full_name": { + "description": "a long-form human readable name for a thing", + "type": "string" + }, + "generated": { + "items": { + "$ref": "#/$defs/BarcodedCellSample" + }, + "type": "array" + }, "has_attribute": { "description": "connects any entity to an attribute", "items": { @@ -3554,61 +3640,81 @@ "description": "A human-readable name for an attribute or entity.", "type": "string" }, + "provided_by": { + "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", + "items": { + "type": "string" + }, + "type": "array" + }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" }, "type": "array" }, - "value": { - "type": "string" + "used": { + "items": { + "$ref": "#/$defs/EnrichedCellSample" + }, + "type": "array" + }, + "wasAssociatedWith": { + "items": { + "$ref": "#/$defs/Agent" + }, + "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" } }, "required": [ - "id" + "id", + "category" ], - "title": "Checksum", + "title": "CellBarcoding", "type": "object" }, - "ChemicalAffectsGeneAssociation": { + "CellDissociation": { "additionalProperties": false, - "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.)", + "description": "A process that takes a tissue sample and produces a dissociated cell sample.", "properties": { - "aggregator_knowledge_source": { - "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", - "items": { - "type": "string" - }, - "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" - }, "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" }, - "causal_mechanism_qualifier": { - "$ref": "#/$defs/CausalMechanismQualifierEnum", - "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')" - }, "description": { "description": "a human-readable description of an entity", "type": "string" }, - "has_attribute": { - "description": "connects any entity to an attribute", + "full_name": { + "description": "a long-form human readable name for a thing", + "type": "string" + }, + "generated": { "items": { - "type": "string" + "$ref": "#/$defs/DissociatedCellSample" }, "type": "array" }, - "has_evidence": { - "description": "connects an association to an instance of supporting evidence", + "has_attribute": { + "description": "connects any entity to an attribute", "items": { "type": "string" }, @@ -3622,166 +3728,136 @@ "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "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" - }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" }, - "negated": { - "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" - }, - "object": { - "$ref": "#/$defs/GeneOrGeneProduct", - "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." - }, - "object_aspect_qualifier": { - "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum" - }, - "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" - }, - "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.", + "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" }, - "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.", + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, "type": "array" }, - "object_context_qualifier": { - "type": "string" - }, - "object_form_or_variant_qualifier": { - "$ref": "#/$defs/ChemicalOrGeneOrGeneProductFormOrVariantEnum" - }, - "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.", + "type": { "items": { "type": "string" }, "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" - }, - "object_part_qualifier": { - "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum" - }, - "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" - }, - "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" - }, - "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" - }, - "predicate": { - "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", - "type": "string" + "used": { + "items": { + "$ref": "#/$defs/TissueSample" + }, + "type": "array" }, - "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" + "wasAssociatedWith": { + "items": { + "$ref": "#/$defs/Agent" + }, + "type": "array" }, - "publications": { - "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", + "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" - }, - "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.", + } + }, + "required": [ + "id", + "category" + ], + "title": "CellDissociation", + "type": "object" + }, + "CellEnrichment": { + "additionalProperties": false, + "description": "A process that takes a dissociated cell sample and produces an enriched cell sample.", + "properties": { + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", "type": "string" }, - "qualifiers": { - "description": "connects an association to qualifiers that modify or qualify the meaning of that association", + "full_name": { + "description": "a long-form human readable name for a thing", + "type": "string" + }, + "generated": { "items": { - "type": "string" + "$ref": "#/$defs/EnrichedCellSample" }, "type": "array" }, - "retrieval_source_ids": { - "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", + "has_attribute": { + "description": "connects any entity to an attribute", "items": { "type": "string" }, "type": "array" }, - "subject": { - "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, - "subject_aspect_qualifier": { - "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum" + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "type": "string" }, - "subject_category": { - "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", + "name": { + "description": "A human-readable name for an attribute or entity.", "type": "string" }, - "subject_category_closure": { - "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", + "provided_by": { + "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, "type": "array" }, - "subject_closure": { - "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, "type": "array" }, - "subject_context_qualifier": { - "type": "string" - }, - "subject_derivative_qualifier": { - "$ref": "#/$defs/ChemicalEntityDerivativeEnum" - }, - "subject_direction_qualifier": { - "$ref": "#/$defs/DirectionQualifierEnum" - }, - "subject_form_or_variant_qualifier": { - "$ref": "#/$defs/ChemicalOrGeneOrGeneProductFormOrVariantEnum" - }, - "subject_label_closure": { - "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", + "type": { "items": { "type": "string" }, "type": "array" }, - "subject_namespace": { - "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" - }, - "subject_part_qualifier": { - "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum" + "used": { + "items": { + "$ref": "#/$defs/DissociatedCellSample" + }, + "type": "array" }, - "timepoint": { - "description": "a point in time", - "format": "time", - "type": "string" + "wasAssociatedWith": { + "items": { + "$ref": "#/$defs/Agent" + }, + "type": "array" }, - "type": { - "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", + "xref": { + "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, @@ -3789,25 +3865,16 @@ } }, "required": [ - "subject", - "predicate", - "object", - "id" + "id", + "category" ], - "title": "ChemicalAffectsGeneAssociation", + "title": "CellEnrichment", "type": "object" }, - "ChemicalEntity": { + "CellLine": { "additionalProperties": false, - "description": "A chemical entity is a physical entity that pertains to chemistry or biochemistry.", + "description": "", "properties": { - "available_from": { - "description": "", - "items": { - "$ref": "#/$defs/DrugAvailabilityEnum" - }, - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { @@ -3825,35 +3892,31 @@ "type": "string" }, "has_attribute": { - "description": "connects any entity to an attribute", + "description": "may often be an organism attribute", "items": { "type": "string" }, "type": "array" }, - "has_chemical_role": { - "description": "A role is particular behaviour which a chemical entity may exhibit.", + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "in_taxon": { + "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": { "type": "string" }, "type": "array" }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "in_taxon_label": { + "description": "The human readable scientific name for the taxon of the entity.", "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "is_toxic": { - "description": "", - "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" - }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" @@ -3865,9 +3928,12 @@ }, "type": "array" }, - "trade_name": { - "description": "", - "type": "string" + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" }, "type": { "items": { @@ -3887,10 +3953,10 @@ "id", "category" ], - "title": "ChemicalEntity", + "title": "CellLine", "type": "object" }, - "ChemicalEntityAssessesNamedThingAssociation": { + "CellLineAsAModelOfDiseaseAssociation": { "additionalProperties": false, "description": "", "properties": { @@ -3912,6 +3978,10 @@ "description": "a human-readable description of an entity", "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" + }, "has_attribute": { "description": "connects any entity to an attribute", "items": { @@ -3947,7 +4017,7 @@ "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.", + "description": "disease", "type": "string" }, "object_category": { @@ -3979,6 +4049,10 @@ "description": "Used to 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" }, + "onset_qualifier": { + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "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" @@ -3992,7 +4066,7 @@ "type": "string" }, "predicate": { - "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", + "description": "The relationship to the disease", "type": "string" }, "primary_knowledge_source": { @@ -4020,8 +4094,12 @@ }, "type": "array" }, + "severity_qualifier": { + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "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.", + "description": "A cell line derived from an organismal entity with a disease state that is used as a model of that disease.", "type": "string" }, "subject_category": { @@ -4072,20 +4150,12 @@ "object", "id" ], - "title": "ChemicalEntityAssessesNamedThingAssociation", + "title": "CellLineAsAModelOfDiseaseAssociation", "type": "object" }, - "ChemicalEntityDerivativeEnum": { - "description": "", - "enum": [ - "metabolite" - ], - "title": "ChemicalEntityDerivativeEnum", - "type": "string" - }, - "ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation": { + "CellLineToDiseaseOrPhenotypicFeatureAssociation": { "additionalProperties": false, - "description": "A regulatory relationship between two genes", + "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.", "properties": { "aggregator_knowledge_source": { "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", @@ -4140,8 +4210,8 @@ "type": "boolean" }, "object": { - "$ref": "#/$defs/GeneOrGeneProduct", - "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." + "description": "disease or phenotype", + "type": "string" }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -4161,9 +4231,6 @@ }, "type": "array" }, - "object_direction_qualifier": { - "$ref": "#/$defs/DirectionQualifierEnum" - }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { @@ -4188,7 +4255,7 @@ "type": "string" }, "predicate": { - "description": "the direction is always from regulator to regulated", + "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string" }, "primary_knowledge_source": { @@ -4217,8 +4284,8 @@ "type": "array" }, "subject": { - "$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", - "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." + "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.", + "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.", @@ -4268,12 +4335,12 @@ "object", "id" ], - "title": "ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation", + "title": "CellLineToDiseaseOrPhenotypicFeatureAssociation", "type": "object" }, - "ChemicalExposure": { + "CellularComponent": { "additionalProperties": false, - "description": "A chemical exposure is an intake of a particular chemical entity.", + "description": "A location in or around a cell", "properties": { "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -4292,29 +4359,25 @@ "type": "string" }, "has_attribute": { - "description": "connects any entity to an attribute", + "description": "may often be an organism attribute", "items": { "type": "string" }, "type": "array" }, - "has_attribute_type": { - "description": "connects an attribute to a class that describes it", - "type": "string" - }, - "has_qualitative_value": { - "description": "connects an attribute to a value", + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, - "has_quantitative_value": { - "description": "connects an attribute to a value", + "in_taxon": { + "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": { - "$ref": "#/$defs/QuantityValue" + "type": "string" }, "type": "array" }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "in_taxon_label": { + "description": "The human readable scientific name for the taxon of the entity.", "type": "string" }, "iri": { @@ -4322,7 +4385,7 @@ "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.", + "description": "A human-readable name for an attribute or entity.", "type": "string" }, "provided_by": { @@ -4332,10 +4395,12 @@ }, "type": "array" }, - "timepoint": { - "description": "a point in time", - "format": "time", - "type": "string" + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" }, "type": { "items": { @@ -4352,31 +4417,20 @@ } }, "required": [ - "has_attribute_type", "id", "category" ], - "title": "ChemicalExposure", + "title": "CellularComponent", "type": "object" }, - "ChemicalGeneInteractionAssociation": { + "CellularOrganism": { "additionalProperties": false, - "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)", + "description": "", "properties": { - "aggregator_knowledge_source": { - "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", - "items": { - "type": "string" - }, - "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" - }, "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" @@ -4385,19 +4439,173 @@ "description": "a human-readable description of an entity", "type": "string" }, + "full_name": { + "description": "a long-form human readable name for a thing", + "type": "string" + }, "has_attribute": { - "description": "connects any entity to an attribute", + "description": "may often be an organism attribute", "items": { "type": "string" }, "type": "array" }, - "has_evidence": { - "description": "connects an association to an instance of supporting evidence", - "items": { - "type": "string" - }, - "type": "array" + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "in_taxon": { + "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", + "items": { + "type": "string" + }, + "type": "array" + }, + "in_taxon_label": { + "description": "The human readable scientific name for the taxon of the entity.", + "type": "string" + }, + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "type": "string" + }, + "name": { + "description": "A human-readable name for an attribute or entity.", + "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" + }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, + "type": { + "items": { + "type": "string" + }, + "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" + } + }, + "required": [ + "id", + "category" + ], + "title": "CellularOrganism", + "type": "object" + }, + "Checksum": { + "additionalProperties": false, + "description": "Checksum values associated with digital entities.", + "properties": { + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "type": "string" + }, + "type": "array" + }, + "checksum_algorithm": { + "$ref": "#/$defs/DigestType", + "description": "The type of cryptographic hash function used to calculate the checksum value." + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "type": "string" + }, + "name": { + "description": "A human-readable name for an attribute or entity.", + "type": "string" + }, + "type": { + "items": { + "type": "string" + }, + "type": "array" + }, + "value": { + "description": "The checksum value obtained from a specific cryotographic hash function.", + "type": "string" + } + }, + "required": [ + "id" + ], + "title": "Checksum", + "type": "object" + }, + "ChemicalAffectsGeneAssociation": { + "additionalProperties": false, + "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.)", + "properties": { + "aggregator_knowledge_source": { + "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", + "items": { + "type": "string" + }, + "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" + }, + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "type": "string" + }, + "type": "array" + }, + "causal_mechanism_qualifier": { + "$ref": "#/$defs/CausalMechanismQualifierEnum", + "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')" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_evidence": { + "description": "connects an association to an instance of supporting evidence", + "items": { + "type": "string" + }, + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -4423,6 +4631,9 @@ "$ref": "#/$defs/GeneOrGeneProduct", "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." }, + "object_aspect_qualifier": { + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum" + }, "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" @@ -4488,6 +4699,10 @@ }, "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" + }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { @@ -4503,9 +4718,12 @@ "type": "array" }, "subject": { - "description": "the chemical entity or entity that is an interactor", + "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.", "type": "string" }, + "subject_aspect_qualifier": { + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum" + }, "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" @@ -4530,6 +4748,9 @@ "subject_derivative_qualifier": { "$ref": "#/$defs/ChemicalEntityDerivativeEnum" }, + "subject_direction_qualifier": { + "$ref": "#/$defs/DirectionQualifierEnum" + }, "subject_form_or_variant_qualifier": { "$ref": "#/$defs/ChemicalOrGeneOrGeneProductFormOrVariantEnum" }, @@ -4566,12 +4787,12 @@ "object", "id" ], - "title": "ChemicalGeneInteractionAssociation", + "title": "ChemicalAffectsGeneAssociation", "type": "object" }, - "ChemicalMixture": { + "ChemicalEntity": { "additionalProperties": false, - "description": "A chemical mixture is a chemical entity composed of two or more molecular entities.", + "description": "A chemical entity is a physical entity that pertains to chemistry or biochemistry.", "properties": { "available_from": { "description": "", @@ -4592,10 +4813,6 @@ "description": "a human-readable description of an entity", "type": "string" }, - "drug_regulatory_status_world_wide": { - "description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", - "type": "string" - }, "full_name": { "description": "a long-form human readable name for a thing", "type": "string" @@ -4614,10 +4831,6 @@ }, "type": "array" }, - "highest_FDA_approval_status": { - "description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", - "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" @@ -4626,10 +4839,6 @@ "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "is_supplement": { - "description": "", - "type": "string" - }, "is_toxic": { "description": "", "type": "boolean" @@ -4649,10 +4858,10 @@ }, "type": "array" }, - "routes_of_delivery": { - "description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { - "$ref": "#/$defs/DrugDeliveryEnum" + "type": "string" }, "type": "array" }, @@ -4678,17 +4887,13 @@ "id", "category" ], - "title": "ChemicalMixture", + "title": "ChemicalEntity", "type": "object" }, - "ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation": { + "ChemicalEntityAssessesNamedThingAssociation": { "additionalProperties": false, - "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.", + "description": "", "properties": { - "FDA_adverse_event_level": { - "$ref": "#/$defs/FDAIDAAdverseEventEnum", - "description": "" - }, "aggregator_knowledge_source": { "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": { @@ -4742,7 +4947,7 @@ "type": "boolean" }, "object": { - "description": "disease or phenotype", + "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string" }, "object_category": { @@ -4816,8 +5021,8 @@ "type": "array" }, "subject": { - "$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", - "description": "the chemical entity or entity that is an interactor" + "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.", + "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.", @@ -4867,17 +5072,21 @@ "object", "id" ], - "title": "ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation", + "title": "ChemicalEntityAssessesNamedThingAssociation", "type": "object" }, - "ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation": { + "ChemicalEntityDerivativeEnum": { + "description": "", + "enum": [ + "metabolite" + ], + "title": "ChemicalEntityDerivativeEnum", + "type": "string" + }, + "ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation": { "additionalProperties": false, - "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.", + "description": "A regulatory relationship between two genes", "properties": { - "FDA_adverse_event_level": { - "$ref": "#/$defs/FDAIDAAdverseEventEnum", - "description": "" - }, "aggregator_knowledge_source": { "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": { @@ -4931,8 +5140,8 @@ "type": "boolean" }, "object": { - "description": "disease or phenotype", - "type": "string" + "$ref": "#/$defs/GeneOrGeneProduct", + "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." }, "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.", @@ -4952,6 +5161,9 @@ }, "type": "array" }, + "object_direction_qualifier": { + "$ref": "#/$defs/DirectionQualifierEnum" + }, "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": { @@ -4976,7 +5188,7 @@ "type": "string" }, "predicate": { - "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", + "description": "the direction is always from regulator to regulated", "type": "string" }, "primary_knowledge_source": { @@ -5006,7 +5218,7 @@ }, "subject": { "$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", - "description": "the chemical entity or entity that is an interactor" + "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." }, "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.", @@ -5056,26 +5268,12 @@ "object", "id" ], - "title": "ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation", + "title": "ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation", "type": "object" }, - "ChemicalOrGeneOrGeneProductFormOrVariantEnum": { - "description": "", - "enum": [ - "genetic_variant_form", - "modified_form", - "loss_of_function_variant_form", - "gain_of_function_variant_form", - "polymorphic_form", - "snp_form", - "analog_form" - ], - "title": "ChemicalOrGeneOrGeneProductFormOrVariantEnum", - "type": "string" - }, - "ChemicalRole": { + "ChemicalExposure": { "additionalProperties": false, - "description": "A role played by the molecular entity or part thereof within a chemical context.", + "description": "A chemical exposure is an intake of a particular chemical entity.", "properties": { "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -5134,6 +5332,18 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, + "timepoint": { + "description": "a point in time", + "format": "time", + "type": "string" + }, "type": { "items": { "type": "string" @@ -5153,12 +5363,12 @@ "id", "category" ], - "title": "ChemicalRole", + "title": "ChemicalExposure", "type": "object" }, - "ChemicalToChemicalAssociation": { + "ChemicalGeneInteractionAssociation": { "additionalProperties": false, - "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.", + "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)", "properties": { "aggregator_knowledge_source": { "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", @@ -5167,6 +5377,10 @@ }, "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" + }, "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { @@ -5213,8 +5427,8 @@ "type": "boolean" }, "object": { - "description": "the chemical element that is the target of the statement", - "type": "string" + "$ref": "#/$defs/GeneOrGeneProduct", + "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." }, "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.", @@ -5234,6 +5448,12 @@ }, "type": "array" }, + "object_context_qualifier": { + "type": "string" + }, + "object_form_or_variant_qualifier": { + "$ref": "#/$defs/ChemicalOrGeneOrGeneProductFormOrVariantEnum" + }, "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": { @@ -5245,6 +5465,9 @@ "description": "Used to 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" }, + "object_part_qualifier": { + "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum" + }, "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" @@ -5287,8 +5510,8 @@ "type": "array" }, "subject": { - "$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", - "description": "the chemical entity or entity that is an interactor" + "description": "the chemical entity or entity that is an interactor", + "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.", @@ -5308,6 +5531,15 @@ }, "type": "array" }, + "subject_context_qualifier": { + "type": "string" + }, + "subject_derivative_qualifier": { + "$ref": "#/$defs/ChemicalEntityDerivativeEnum" + }, + "subject_form_or_variant_qualifier": { + "$ref": "#/$defs/ChemicalOrGeneOrGeneProductFormOrVariantEnum" + }, "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": { @@ -5319,6 +5551,9 @@ "description": "Used to 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" }, + "subject_part_qualifier": { + "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum" + }, "timepoint": { "description": "a point in time", "format": "time", @@ -5338,30 +5573,24 @@ "object", "id" ], - "title": "ChemicalToChemicalAssociation", + "title": "ChemicalGeneInteractionAssociation", "type": "object" }, - "ChemicalToChemicalDerivationAssociation": { + "ChemicalMixture": { "additionalProperties": false, - "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:\n IF\n R has-input C1 AND\n R has-output C2 AND\n R enabled-by P AND\n R type Reaction\n THEN\n C1 derives-into C2 <>", + "description": "A chemical mixture is a chemical entity composed of two or more molecular entities.", "properties": { - "aggregator_knowledge_source": { - "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", - "items": { - "type": "string" - }, - "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.", + "available_from": { + "description": "", "items": { - "$ref": "#/$defs/MacromolecularMachineMixin" + "$ref": "#/$defs/DrugAvailabilityEnum" }, "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" @@ -5370,6 +5599,14 @@ "description": "a human-readable description of an entity", "type": "string" }, + "drug_regulatory_status_world_wide": { + "description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", + "type": "string" + }, + "full_name": { + "description": "a long-form human readable name for a thing", + "type": "string" + }, "has_attribute": { "description": "connects any entity to an attribute", "items": { @@ -5377,13 +5614,17 @@ }, "type": "array" }, - "has_evidence": { - "description": "connects an association to an instance of supporting evidence", + "has_chemical_role": { + "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, "type": "array" }, + "highest_FDA_approval_status": { + "description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", + "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" @@ -5392,132 +5633,55 @@ "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "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" - }, - "name": { - "description": "A human-readable name for an attribute or entity.", + "is_supplement": { + "description": "", "type": "string" }, - "negated": { - "description": "if set to true, then the association is negated i.e. is not true", + "is_toxic": { + "description": "", "type": "boolean" }, - "object": { - "description": "the downstream chemical entity", - "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" - }, - "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" - }, - "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" - }, - "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" - }, - "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" - }, - "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" - }, - "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" - }, - "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" - }, - "predicate": { - "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", + "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" }, - "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.", + "name": { + "description": "A human-readable name for an attribute or entity.", "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.", + "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" }, - "qualifiers": { - "description": "connects an association to qualifiers that modify or qualify the meaning of that association", + "routes_of_delivery": { + "description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": { - "type": "string" + "$ref": "#/$defs/DrugDeliveryEnum" }, "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.", + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, "type": "array" }, - "subject": { - "description": "the upstream chemical entity", - "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.", + "trade_name": { + "description": "", "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" - }, - "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" - }, - "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.", + "type": { "items": { "type": "string" }, "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" - }, - "timepoint": { - "description": "a point in time", - "format": "time", - "type": "string" - }, - "type": { - "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", + "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" }, @@ -5525,18 +5689,20 @@ } }, "required": [ - "subject", - "predicate", - "object", - "id" + "id", + "category" ], - "title": "ChemicalToChemicalDerivationAssociation", + "title": "ChemicalMixture", "type": "object" }, - "ChemicalToDiseaseOrPhenotypicFeatureAssociation": { + "ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation": { "additionalProperties": false, - "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.", + "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.", "properties": { + "FDA_adverse_event_level": { + "$ref": "#/$defs/FDAIDAAdverseEventEnum", + "description": "" + }, "aggregator_knowledge_source": { "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": { @@ -5590,7 +5756,7 @@ "type": "boolean" }, "object": { - "description": "the disease or phenotype that is affected by the chemical", + "description": "disease or phenotype", "type": "string" }, "object_category": { @@ -5715,13 +5881,17 @@ "object", "id" ], - "title": "ChemicalToDiseaseOrPhenotypicFeatureAssociation", + "title": "ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation", "type": "object" }, - "ChemicalToPathwayAssociation": { + "ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation": { "additionalProperties": false, - "description": "An interaction between a chemical entity and a biological process or pathway.", + "description": "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect.", "properties": { + "FDA_adverse_event_level": { + "$ref": "#/$defs/FDAIDAAdverseEventEnum", + "description": "" + }, "aggregator_knowledge_source": { "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": { @@ -5775,7 +5945,7 @@ "type": "boolean" }, "object": { - "description": "the pathway that is affected by the chemical", + "description": "disease or phenotype", "type": "string" }, "object_category": { @@ -5849,8 +6019,8 @@ "type": "array" }, "subject": { - "description": "the chemical entity that is affecting the pathway", - "type": "string" + "$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", + "description": "the chemical entity or entity that is an interactor" }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -5900,93 +6070,26 @@ "object", "id" ], - "title": "ChemicalToPathwayAssociation", + "title": "ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation", "type": "object" }, - "ChiSquaredAnalysisResult": { - "additionalProperties": false, - "description": "A result of a chi squared analysis.", - "properties": { - "category": { - "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", - "items": { - "pattern": "^biolink:[A-Z][A-Za-z]+$", - "type": "string" - }, - "type": "array" - }, - "creation_date": { - "description": "date on which an entity was created. This can be applied to nodes or edges", - "format": "date", - "type": "string" - }, - "description": { - "description": "a human-readable description of an entity", - "type": "string" - }, - "format": { - "type": "string" - }, - "full_name": { - "description": "a long-form human readable name for a thing", - "type": "string" - }, - "has_attribute": { - "description": "connects any entity to an attribute", - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", - "type": "string" - }, - "iri": { - "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" - }, - "license": { - "type": "string" - }, - "name": { - "description": "A human-readable name for an attribute or entity.", - "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" - }, - "rights": { - "type": "string" - }, - "type": { - "items": { - "type": "string" - }, - "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" - } - }, - "required": [ - "id", - "category" + "ChemicalOrGeneOrGeneProductFormOrVariantEnum": { + "description": "", + "enum": [ + "genetic_variant_form", + "modified_form", + "loss_of_function_variant_form", + "gain_of_function_variant_form", + "polymorphic_form", + "snp_form", + "analog_form" ], - "title": "ChiSquaredAnalysisResult", - "type": "object" + "title": "ChemicalOrGeneOrGeneProductFormOrVariantEnum", + "type": "string" }, - "ClinicalAttribute": { + "ChemicalRole": { "additionalProperties": false, - "description": "Attributes relating to a clinical manifestation", + "description": "A role played by the molecular entity or part thereof within a chemical context.", "properties": { "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -6045,6 +6148,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -6064,17 +6174,23 @@ "id", "category" ], - "title": "ClinicalAttribute", + "title": "ChemicalRole", "type": "object" }, - "ClinicalCourse": { + "ChemicalToChemicalAssociation": { "additionalProperties": false, - "description": "The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual", + "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.", "properties": { + "aggregator_knowledge_source": { + "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", + "items": { + "type": "string" + }, + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { - "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" @@ -6083,10 +6199,6 @@ "description": "a human-readable description of an entity", "type": "string" }, - "full_name": { - "description": "a long-form human readable name for a thing", - "type": "string" - }, "has_attribute": { "description": "connects any entity to an attribute", "items": { @@ -6094,18 +6206,10 @@ }, "type": "array" }, - "has_attribute_type": { - "description": "connects an attribute to a class that describes it", - "type": "string" - }, - "has_qualitative_value": { - "description": "connects an attribute to a value", - "type": "string" - }, - "has_quantitative_value": { - "description": "connects an attribute to a value", + "has_evidence": { + "description": "connects an association to an instance of supporting evidence", "items": { - "$ref": "#/$defs/QuantityValue" + "type": "string" }, "type": "array" }, @@ -6117,171 +6221,132 @@ "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, + "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" + }, "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.", + "description": "A human-readable name for an attribute or entity.", "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" + "negated": { + "description": "if set to true, then the association is negated i.e. is not true", + "type": "boolean" }, - "type": { + "object": { + "description": "the chemical element that is the target of the statement", + "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" + }, + "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" }, - "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.", + "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" - } - }, - "required": [ - "has_attribute_type", - "id", - "category" - ], - "title": "ClinicalCourse", - "type": "object" - }, - "ClinicalEntity": { - "additionalProperties": false, - "description": "Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities", - "properties": { - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + }, + "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": { - "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" }, - "description": { - "description": "a human-readable description of an entity", + "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" }, - "full_name": { - "description": "a long-form human readable name for a thing", + "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" }, - "has_attribute": { - "description": "connects any entity to an attribute", - "items": { - "type": "string" - }, - "type": "array" + "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" }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "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" }, - "iri": { - "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "predicate": { + "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string" }, - "name": { - "description": "A human-readable name for an attribute or entity.", + "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" }, - "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.", + "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" }, - "type": { + "qualifiers": { + "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, "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" - } - }, - "required": [ - "id", - "category" - ], - "title": "ClinicalEntity", - "type": "object" - }, - "ClinicalFinding": { - "additionalProperties": false, - "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.", - "properties": { - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "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": { - "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" }, - "description": { - "description": "a human-readable description of an entity", - "type": "string" + "subject": { + "$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", + "description": "the chemical entity or entity that is an interactor" }, - "full_name": { - "description": "a long-form human readable name for a thing", + "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" }, - "has_attribute": { - "description": "connects any entity to an attribute", + "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" }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", - "type": "string" + "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" }, - "in_taxon": { - "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", + "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" }, - "in_taxon_label": { - "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" - }, - "iri": { - "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "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" }, - "name": { - "description": "A human-readable name for an attribute or entity.", + "timepoint": { + "description": "a point in time", + "format": "time", "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" - }, "type": { - "items": { - "type": "string" - }, - "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.", + "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, @@ -6289,20 +6354,35 @@ } }, "required": [ - "id", - "category" + "subject", + "predicate", + "object", + "id" ], - "title": "ClinicalFinding", + "title": "ChemicalToChemicalAssociation", "type": "object" }, - "ClinicalIntervention": { + "ChemicalToChemicalDerivationAssociation": { "additionalProperties": false, - "description": "", + "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:\n IF\n R has-input C1 AND\n R has-output C2 AND\n R enabled-by P AND\n R type Reaction\n THEN\n C1 derives-into C2 <>", "properties": { + "aggregator_knowledge_source": { + "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", + "items": { + "type": "string" + }, + "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": "#/$defs/MacromolecularMachineMixin" + }, + "type": "array" + }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { - "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" @@ -6311,10 +6391,6 @@ "description": "a human-readable description of an entity", "type": "string" }, - "full_name": { - "description": "a long-form human readable name for a thing", - "type": "string" - }, "has_attribute": { "description": "connects any entity to an attribute", "items": { @@ -6322,6 +6398,13 @@ }, "type": "array" }, + "has_evidence": { + "description": "connects an association to an instance of supporting evidence", + "items": { + "type": "string" + }, + "type": "array" + }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" @@ -6330,107 +6413,132 @@ "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, + "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" + }, "name": { "description": "A human-readable name for an attribute or entity.", "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" + "negated": { + "description": "if set to true, then the association is negated i.e. is not true", + "type": "boolean" }, - "type": { + "object": { + "description": "the downstream chemical entity", + "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" + }, + "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" }, - "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.", + "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" - } - }, - "required": [ - "id", - "category" - ], - "title": "ClinicalIntervention", - "type": "object" - }, - "ClinicalMeasurement": { - "additionalProperties": false, - "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.", - "properties": { - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + }, + "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": { - "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" }, - "description": { - "description": "a human-readable description of an entity", + "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" }, - "full_name": { - "description": "a long-form human readable name for a thing", + "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" }, - "has_attribute": { - "description": "connects any entity to an attribute", + "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" + }, + "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" + }, + "predicate": { + "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", + "type": "string" + }, + "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" + }, + "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" }, - "has_attribute_type": { - "description": "connects an attribute to a class that describes it", - "type": "string" - }, - "has_qualitative_value": { - "description": "connects an attribute to a value", - "type": "string" + "qualifiers": { + "description": "connects an association to qualifiers that modify or qualify the meaning of that association", + "items": { + "type": "string" + }, + "type": "array" }, - "has_quantitative_value": { - "description": "connects an attribute to a value", + "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": { - "$ref": "#/$defs/QuantityValue" + "type": "string" }, "type": "array" }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "subject": { + "description": "the upstream chemical entity", "type": "string" }, - "iri": { - "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "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" }, - "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" + "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" }, - "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.", + "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" }, - "type": { + "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" }, - "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.", + "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" + }, + "timepoint": { + "description": "a point in time", + "format": "time", + "type": "string" + }, + "type": { + "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, @@ -6438,21 +6546,28 @@ } }, "required": [ - "has_attribute_type", - "id", - "category" + "subject", + "predicate", + "object", + "id" ], - "title": "ClinicalMeasurement", + "title": "ChemicalToChemicalDerivationAssociation", "type": "object" }, - "ClinicalModifier": { + "ChemicalToDiseaseOrPhenotypicFeatureAssociation": { "additionalProperties": false, - "description": "Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects", + "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.", "properties": { + "aggregator_knowledge_source": { + "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", + "items": { + "type": "string" + }, + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { - "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" @@ -6461,10 +6576,6 @@ "description": "a human-readable description of an entity", "type": "string" }, - "full_name": { - "description": "a long-form human readable name for a thing", - "type": "string" - }, "has_attribute": { "description": "connects any entity to an attribute", "items": { @@ -6472,18 +6583,10 @@ }, "type": "array" }, - "has_attribute_type": { - "description": "connects an attribute to a class that describes it", - "type": "string" - }, - "has_qualitative_value": { - "description": "connects an attribute to a value", - "type": "string" - }, - "has_quantitative_value": { - "description": "connects an attribute to a value", + "has_evidence": { + "description": "connects an association to an instance of supporting evidence", "items": { - "$ref": "#/$defs/QuantityValue" + "type": "string" }, "type": "array" }, @@ -6495,205 +6598,132 @@ "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, + "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" + }, "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.", + "description": "A human-readable name for an attribute or entity.", "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" + "negated": { + "description": "if set to true, then the association is negated i.e. is not true", + "type": "boolean" }, - "type": { - "items": { - "type": "string" - }, - "type": "array" + "object": { + "description": "the disease or phenotype that is affected by the chemical", + "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.", + "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" + }, + "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" - } - }, - "required": [ - "has_attribute_type", - "id", - "category" - ], - "title": "ClinicalModifier", - "type": "object" - }, - "ClinicalTrial": { - "additionalProperties": false, - "description": "", - "properties": { - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + }, + "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": { - "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" }, - "description": { - "description": "a human-readable description of an entity", - "type": "string" - }, - "full_name": { - "description": "a long-form human readable name for a thing", - "type": "string" - }, - "has_attribute": { - "description": "connects any entity to an attribute", + "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" }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "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" }, - "iri": { - "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "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" }, - "name": { - "description": "A human-readable name for an attribute or entity.", + "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" }, - "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" + "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" }, - "type": { + "predicate": { + "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", + "type": "string" + }, + "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" + }, + "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" }, - "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.", + "qualifiers": { + "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, "type": "array" - } - }, - "required": [ - "id", - "category" - ], - "title": "ClinicalTrial", - "type": "object" - }, - "CodingSequence": { - "additionalProperties": false, - "description": "", - "properties": { - "available_from": { - "description": "", - "items": { - "$ref": "#/$defs/DrugAvailabilityEnum" - }, - "type": "array" }, - "category": { - "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "retrieval_source_ids": { + "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { - "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" }, - "description": { - "description": "a human-readable description of an entity", - "type": "string" + "subject": { + "$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", + "description": "the chemical entity or entity that is an interactor" }, - "full_name": { - "description": "a long-form human readable name for a thing", + "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" }, - "has_attribute": { - "description": "connects any entity to an attribute", + "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" }, - "has_biological_sequence": { - "description": "connects a genomic feature to its sequence", - "type": "string" - }, - "has_chemical_role": { - "description": "A role is particular behaviour which a chemical entity may exhibit.", + "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" }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", - "type": "string" - }, - "in_taxon": { - "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", + "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" }, - "in_taxon_label": { - "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" - }, - "iri": { - "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" - }, - "is_metabolite": { - "description": "indicates whether a molecular entity is a metabolite", - "type": "boolean" - }, - "is_toxic": { - "description": "", - "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" - }, - "name": { - "description": "A human-readable name for an attribute or entity.", + "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" }, - "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" - }, - "trade_name": { - "description": "", + "timepoint": { + "description": "a point in time", + "format": "time", "type": "string" }, "type": { - "items": { - "type": "string" - }, - "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.", + "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, @@ -6701,20 +6731,28 @@ } }, "required": [ - "id", - "category" + "subject", + "predicate", + "object", + "id" ], - "title": "CodingSequence", + "title": "ChemicalToDiseaseOrPhenotypicFeatureAssociation", "type": "object" }, - "Cohort": { + "ChemicalToPathwayAssociation": { "additionalProperties": false, - "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.", + "description": "An interaction between a chemical entity and a biological process or pathway.", "properties": { + "aggregator_knowledge_source": { + "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", + "items": { + "type": "string" + }, + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { - "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" @@ -6723,73 +6761,174 @@ "description": "a human-readable description of an entity", "type": "string" }, - "full_name": { - "description": "a long-form human readable name for a thing", - "type": "string" - }, "has_attribute": { - "description": "may often be an organism attribute", + "description": "connects any entity to an attribute", "items": { "type": "string" }, "type": "array" }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", - "type": "string" - }, - "in_taxon": { - "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", + "has_evidence": { + "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, "type": "array" }, - "in_taxon_label": { - "description": "The human readable scientific name for the taxon of the entity.", + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, + "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" + }, "name": { "description": "A human-readable name for an attribute or entity.", "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.", + "negated": { + "description": "if set to true, then the association is negated i.e. is not true", + "type": "boolean" + }, + "object": { + "description": "the pathway that is affected by the chemical", + "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" + }, + "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" }, - "type": { + "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" }, - "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.", + "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" - } - }, - "required": [ - "id", - "category" - ], - "title": "Cohort", - "type": "object" - }, - "CommonDataElement": { - "additionalProperties": false, - "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)", - "properties": { - "category": { + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "predicate": { + "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", + "type": "string" + }, + "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" + }, + "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" + }, + "qualifiers": { + "description": "connects an association to qualifiers that modify or qualify the meaning of that association", + "items": { + "type": "string" + }, + "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" + }, + "subject": { + "description": "the chemical entity that is affecting the pathway", + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "timepoint": { + "description": "a point in time", + "format": "time", + "type": "string" + }, + "type": { + "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", + "items": { + "type": "string" + }, + "type": "array" + } + }, + "required": [ + "subject", + "predicate", + "object", + "id" + ], + "title": "ChemicalToPathwayAssociation", + "type": "object" + }, + "ChiSquaredAnalysisResult": { + "additionalProperties": false, + "description": "A result of a chi squared analysis.", + "properties": { + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { "pattern": "^biolink:[A-Z][A-Za-z]+$", @@ -6845,6 +6984,13 @@ "rights": { "type": "string" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -6863,12 +7009,12 @@ "id", "category" ], - "title": "CommonDataElement", + "title": "ChiSquaredAnalysisResult", "type": "object" }, - "ComplexChemicalExposure": { + "ClinicalAttribute": { "additionalProperties": false, - "description": "A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug.", + "description": "Attributes relating to a clinical manifestation", "properties": { "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -6927,6 +7073,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -6946,20 +7099,13 @@ "id", "category" ], - "title": "ComplexChemicalExposure", + "title": "ClinicalAttribute", "type": "object" }, - "ComplexMolecularMixture": { + "ClinicalCourse": { "additionalProperties": false, - "description": "A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry.", + "description": "The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual", "properties": { - "available_from": { - "description": "", - "items": { - "$ref": "#/$defs/DrugAvailabilityEnum" - }, - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { @@ -6972,10 +7118,6 @@ "description": "a human-readable description of an entity", "type": "string" }, - "drug_regulatory_status_world_wide": { - "description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", - "type": "string" - }, "full_name": { "description": "a long-form human readable name for a thing", "type": "string" @@ -6987,17 +7129,21 @@ }, "type": "array" }, - "has_chemical_role": { - "description": "A role is particular behaviour which a chemical entity may exhibit.", + "has_attribute_type": { + "description": "connects an attribute to a class that describes it", + "type": "string" + }, + "has_qualitative_value": { + "description": "connects an attribute to a value", + "type": "string" + }, + "has_quantitative_value": { + "description": "connects an attribute to a value", "items": { - "type": "string" + "$ref": "#/$defs/QuantityValue" }, "type": "array" }, - "highest_FDA_approval_status": { - "description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", - "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" @@ -7006,20 +7152,8 @@ "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "is_supplement": { - "description": "", - "type": "string" - }, - "is_toxic": { - "description": "", - "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" - }, "name": { - "description": "A human-readable name for an attribute or entity.", + "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" }, "provided_by": { @@ -7029,17 +7163,13 @@ }, "type": "array" }, - "routes_of_delivery": { - "description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { - "$ref": "#/$defs/DrugDeliveryEnum" + "type": "string" }, "type": "array" }, - "trade_name": { - "description": "", - "type": "string" - }, "type": { "items": { "type": "string" @@ -7055,15 +7185,16 @@ } }, "required": [ + "has_attribute_type", "id", "category" ], - "title": "ComplexMolecularMixture", + "title": "ClinicalCourse", "type": "object" }, - "ConceptCountAnalysisResult": { + "ClinicalEntity": { "additionalProperties": false, - "description": "A result of a concept count analysis.", + "description": "Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities", "properties": { "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -7073,18 +7204,10 @@ }, "type": "array" }, - "creation_date": { - "description": "date on which an entity was created. This can be applied to nodes or edges", - "format": "date", - "type": "string" - }, "description": { "description": "a human-readable description of an entity", "type": "string" }, - "format": { - "type": "string" - }, "full_name": { "description": "a long-form human readable name for a thing", "type": "string" @@ -7104,9 +7227,6 @@ "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "license": { - "type": "string" - }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" @@ -7118,8 +7238,12 @@ }, "type": "array" }, - "rights": { - "type": "string" + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" }, "type": { "items": { @@ -7139,12 +7263,12 @@ "id", "category" ], - "title": "ConceptCountAnalysisResult", + "title": "ClinicalEntity", "type": "object" }, - "ConfidenceLevel": { + "ClinicalFinding": { "additionalProperties": false, - "description": "Level of confidence in a statement", + "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.", "properties": { "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -7154,18 +7278,10 @@ }, "type": "array" }, - "creation_date": { - "description": "date on which an entity was created. This can be applied to nodes or edges", - "format": "date", - "type": "string" - }, "description": { "description": "a human-readable description of an entity", "type": "string" }, - "format": { - "type": "string" - }, "full_name": { "description": "a long-form human readable name for a thing", "type": "string" @@ -7181,11 +7297,19 @@ "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, - "iri": { - "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "in_taxon": { + "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", + "items": { + "type": "string" + }, + "type": "array" + }, + "in_taxon_label": { + "description": "The human readable scientific name for the taxon of the entity.", "type": "string" }, - "license": { + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, "name": { @@ -7199,8 +7323,12 @@ }, "type": "array" }, - "rights": { - "type": "string" + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" }, "type": { "items": { @@ -7220,23 +7348,17 @@ "id", "category" ], - "title": "ConfidenceLevel", + "title": "ClinicalFinding", "type": "object" }, - "ContributorAssociation": { + "ClinicalIntervention": { "additionalProperties": false, - "description": "Any association between an entity (such as a publication) and various agents that contribute to its realisation", + "description": "", "properties": { - "aggregator_knowledge_source": { - "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", - "items": { - "type": "string" - }, - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" @@ -7245,6 +7367,10 @@ "description": "a human-readable description of an entity", "type": "string" }, + "full_name": { + "description": "a long-form human readable name for a thing", + "type": "string" + }, "has_attribute": { "description": "connects any entity to an attribute", "items": { @@ -7252,13 +7378,6 @@ }, "type": "array" }, - "has_evidence": { - "description": "connects an association to an instance of supporting evidence", - "items": { - "type": "string" - }, - "type": "array" - }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" @@ -7267,132 +7386,121 @@ "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "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" - }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" }, - "negated": { - "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" - }, - "object": { - "description": "agent helping to realise the given entity (e.g. such as a publication)", - "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" - }, - "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.", + "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" }, - "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.", + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, "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.", + "type": { "items": { "type": "string" }, "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" - }, - "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" - }, - "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" - }, - "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" + "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" + } + }, + "required": [ + "id", + "category" + ], + "title": "ClinicalIntervention", + "type": "object" + }, + "ClinicalMeasurement": { + "additionalProperties": false, + "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.", + "properties": { + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", + "type": "string" + }, + "type": "array" }, - "predicate": { - "description": "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'", + "description": { + "description": "a human-readable description of an entity", "type": "string" }, - "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.", + "full_name": { + "description": "a long-form human readable name for a thing", "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.", + "has_attribute": { + "description": "connects any entity to an attribute", "items": { "type": "string" }, "type": "array" }, - "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" + "has_attribute_type": { + "description": "connects an attribute to a class that describes it", + "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.", + "has_qualitative_value": { + "description": "connects an attribute to a value", + "type": "string" + }, + "has_quantitative_value": { + "description": "connects an attribute to a value", "items": { - "type": "string" + "$ref": "#/$defs/QuantityValue" }, "type": "array" }, - "subject": { - "description": "information content entity which an agent has helped realise", + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "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.", + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", "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.", + "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" + }, + "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" }, - "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.", + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, "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.", + "type": { "items": { "type": "string" }, "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" - }, - "timepoint": { - "description": "a point in time", - "format": "time", - "type": "string" - }, - "type": { - "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", + "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" }, @@ -7400,28 +7508,21 @@ } }, "required": [ - "subject", - "predicate", - "object", - "id" + "has_attribute_type", + "id", + "category" ], - "title": "ContributorAssociation", + "title": "ClinicalMeasurement", "type": "object" }, - "CorrelatedGeneToDiseaseAssociation": { + "ClinicalModifier": { "additionalProperties": false, - "description": "", + "description": "Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects", "properties": { - "aggregator_knowledge_source": { - "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", - "items": { - "type": "string" - }, - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" @@ -7430,8 +7531,8 @@ "description": "a human-readable description of an entity", "type": "string" }, - "frequency_qualifier": { - "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", + "full_name": { + "description": "a long-form human readable name for a thing", "type": "string" }, "has_attribute": { @@ -7441,28 +7542,21 @@ }, "type": "array" }, - "has_count": { - "description": "number of things with a particular property", - "type": "integer" + "has_attribute_type": { + "description": "connects an attribute to a class that describes it", + "type": "string" }, - "has_evidence": { - "description": "connects an association to an instance of supporting evidence", + "has_qualitative_value": { + "description": "connects an attribute to a value", + "type": "string" + }, + "has_quantitative_value": { + "description": "connects an attribute to a value", "items": { - "type": "string" + "$ref": "#/$defs/QuantityValue" }, "type": "array" }, - "has_percentage": { - "description": "equivalent to has quotient multiplied by 100", - "type": "number" - }, - "has_quotient": { - "type": "number" - }, - "has_total": { - "description": "total number of things in a particular reference set", - "type": "integer" - }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" @@ -7471,150 +7565,32 @@ "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "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" - }, "name": { - "description": "A human-readable name for an attribute or entity.", - "type": "string" - }, - "negated": { - "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" - }, - "object": { - "description": "disease", - "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.", + "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" }, - "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.", + "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" }, - "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.", + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, "type": "array" }, - "object_direction_qualifier": { - "$ref": "#/$defs/DirectionQualifierEnum" - }, - "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.", + "type": { "items": { "type": "string" }, "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" - }, - "onset_qualifier": { - "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", - "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" - }, - "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" - }, - "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" - }, - "predicate": { - "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", - "type": "string" - }, - "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" - }, - "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" - }, - "qualifiers": { - "description": "connects an association to qualifiers that modify or qualify the meaning of that association", - "items": { - "type": "string" - }, - "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" - }, - "severity_qualifier": { - "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", - "type": "string" - }, - "sex_qualifier": { - "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" - }, - "subject": { - "$ref": "#/$defs/GeneOrGeneProduct", - "description": "gene in which variation is shown to correlate with the disease." - }, - "subject_aspect_qualifier": { - "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum" - }, - "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" - }, - "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" - }, - "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" - }, - "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" - }, - "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" - }, - "timepoint": { - "description": "a point in time", - "format": "time", - "type": "string" - }, - "type": { - "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", + "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" }, @@ -7622,17 +7598,16 @@ } }, "required": [ - "subject", - "predicate", - "object", - "id" + "has_attribute_type", + "id", + "category" ], - "title": "CorrelatedGeneToDiseaseAssociation", + "title": "ClinicalModifier", "type": "object" }, - "Dataset": { + "ClinicalTrial": { "additionalProperties": false, - "description": "an item that refers to a collection of data from a data source.", + "description": "", "properties": { "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -7642,18 +7617,10 @@ }, "type": "array" }, - "creation_date": { - "description": "date on which an entity was created. This can be applied to nodes or edges", - "format": "date", - "type": "string" - }, "description": { "description": "a human-readable description of an entity", "type": "string" }, - "format": { - "type": "string" - }, "full_name": { "description": "a long-form human readable name for a thing", "type": "string" @@ -7673,9 +7640,6 @@ "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "license": { - "type": "string" - }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" @@ -7687,8 +7651,12 @@ }, "type": "array" }, - "rights": { - "type": "string" + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" }, "type": { "items": { @@ -7708,13 +7676,20 @@ "id", "category" ], - "title": "Dataset", + "title": "ClinicalTrial", "type": "object" }, - "DatasetDistribution": { + "CodingSequence": { "additionalProperties": false, - "description": "an item that holds distribution level information about a dataset.", + "description": "", "properties": { + "available_from": { + "description": "", + "items": { + "$ref": "#/$defs/DrugAvailabilityEnum" + }, + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { @@ -7723,21 +7698,10 @@ }, "type": "array" }, - "creation_date": { - "description": "date on which an entity was created. This can be applied to nodes or edges", - "format": "date", - "type": "string" - }, "description": { "description": "a human-readable description of an entity", "type": "string" }, - "distribution_download_url": { - "type": "string" - }, - "format": { - "type": "string" - }, "full_name": { "description": "a long-form human readable name for a thing", "type": "string" @@ -7749,15 +7713,46 @@ }, "type": "array" }, + "has_biological_sequence": { + "description": "connects a genomic feature to its sequence", + "type": "string" + }, + "has_chemical_role": { + "description": "A role is particular behaviour which a chemical entity may exhibit.", + "items": { + "type": "string" + }, + "type": "array" + }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, + "in_taxon": { + "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", + "items": { + "type": "string" + }, + "type": "array" + }, + "in_taxon_label": { + "description": "The human readable scientific name for the taxon of the entity.", + "type": "string" + }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "license": { + "is_metabolite": { + "description": "indicates whether a molecular entity is a metabolite", + "type": "boolean" + }, + "is_toxic": { + "description": "", + "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" }, "name": { @@ -7771,7 +7766,15 @@ }, "type": "array" }, - "rights": { + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, + "trade_name": { + "description": "", "type": "string" }, "type": { @@ -7792,12 +7795,12 @@ "id", "category" ], - "title": "DatasetDistribution", + "title": "CodingSequence", "type": "object" }, - "DatasetSummary": { + "Cohort": { "additionalProperties": false, - "description": "an item that holds summary level information about a dataset.", + "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.", "properties": { "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -7807,24 +7810,16 @@ }, "type": "array" }, - "creation_date": { - "description": "date on which an entity was created. This can be applied to nodes or edges", - "format": "date", - "type": "string" - }, "description": { "description": "a human-readable description of an entity", "type": "string" }, - "format": { - "type": "string" - }, "full_name": { "description": "a long-form human readable name for a thing", "type": "string" }, "has_attribute": { - "description": "connects any entity to an attribute", + "description": "may often be an organism attribute", "items": { "type": "string" }, @@ -7834,11 +7829,19 @@ "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, - "iri": { - "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "in_taxon": { + "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", + "items": { + "type": "string" + }, + "type": "array" + }, + "in_taxon_label": { + "description": "The human readable scientific name for the taxon of the entity.", "type": "string" }, - "license": { + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, "name": { @@ -7852,14 +7855,12 @@ }, "type": "array" }, - "rights": { - "type": "string" - }, - "source_logo": { - "type": "string" - }, - "source_web_page": { - "type": "string" + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" }, "type": { "items": { @@ -7879,12 +7880,12 @@ "id", "category" ], - "title": "DatasetSummary", + "title": "Cohort", "type": "object" }, - "DatasetVersion": { + "CommonDataElement": { "additionalProperties": false, - "description": "an item that holds version level information about a dataset.", + "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)", "properties": { "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -7917,19 +7918,10 @@ }, "type": "array" }, - "has_dataset": { - "type": "string" - }, - "has_distribution": { - "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" - }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" @@ -7951,6 +7943,13 @@ "rights": { "type": "string" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -7969,12 +7968,12 @@ "id", "category" ], - "title": "DatasetVersion", + "title": "CommonDataElement", "type": "object" }, - "Device": { + "ComplexChemicalExposure": { "additionalProperties": false, - "description": "A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment", + "description": "A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug.", "properties": { "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -7999,70 +7998,18 @@ }, "type": "array" }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "has_attribute_type": { + "description": "connects an attribute to a class that describes it", "type": "string" }, - "iri": { - "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" - }, - "name": { - "description": "A human-readable name for an attribute or entity.", - "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" - }, - "type": { - "items": { - "type": "string" - }, - "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" - } - }, - "required": [ - "id", - "category" - ], - "title": "Device", - "type": "object" - }, - "DiagnosticAid": { - "additionalProperties": false, - "description": "A device or substance used to help diagnose disease or injury", - "properties": { - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", - "items": { - "pattern": "^biolink:[A-Z][A-Za-z]+$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of an entity", - "type": "string" - }, - "full_name": { - "description": "a long-form human readable name for a thing", + "has_qualitative_value": { + "description": "connects an attribute to a value", "type": "string" }, - "has_attribute": { - "description": "connects any entity to an attribute", + "has_quantitative_value": { + "description": "connects an attribute to a value", "items": { - "type": "string" + "$ref": "#/$defs/QuantityValue" }, "type": "array" }, @@ -8075,7 +8022,7 @@ "type": "string" }, "name": { - "description": "A human-readable name for an attribute or entity.", + "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" }, "provided_by": { @@ -8085,6 +8032,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -8100,37 +8054,24 @@ } }, "required": [ + "has_attribute_type", "id", "category" ], - "title": "DiagnosticAid", + "title": "ComplexChemicalExposure", "type": "object" }, - "DigestType": { - "description": "", - "enum": [ - "SHA1", - "MD5", - "SHA256" - ], - "title": "DigestType", - "type": "string" - }, - "DirectionQualifierEnum": { - "description": "", - "enum": [ - "increased", - "upregulated", - "decreased", - "downregulated" - ], - "title": "DirectionQualifierEnum", - "type": "string" - }, - "Disease": { + "ComplexMolecularMixture": { "additionalProperties": false, - "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.", + "description": "A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry.", "properties": { + "available_from": { + "description": "", + "items": { + "$ref": "#/$defs/DrugAvailabilityEnum" + }, + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { @@ -8143,6 +8084,10 @@ "description": "a human-readable description of an entity", "type": "string" }, + "drug_regulatory_status_world_wide": { + "description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", + "type": "string" + }, "full_name": { "description": "a long-form human readable name for a thing", "type": "string" @@ -8154,25 +8099,37 @@ }, "type": "array" }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", - "type": "string" - }, - "in_taxon": { - "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", + "has_chemical_role": { + "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, "type": "array" }, - "in_taxon_label": { - "description": "The human readable scientific name for the taxon of the entity.", + "highest_FDA_approval_status": { + "description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", + "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" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, + "is_supplement": { + "description": "", + "type": "string" + }, + "is_toxic": { + "description": "", + "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" + }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" @@ -8184,6 +8141,24 @@ }, "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" + }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, + "trade_name": { + "description": "", + "type": "string" + }, "type": { "items": { "type": "string" @@ -8202,12 +8177,12 @@ "id", "category" ], - "title": "Disease", + "title": "ComplexMolecularMixture", "type": "object" }, - "DiseaseOrPhenotypicFeature": { + "ConceptCountAnalysisResult": { "additionalProperties": false, - "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.", + "description": "A result of a concept count analysis.", "properties": { "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -8217,10 +8192,18 @@ }, "type": "array" }, + "creation_date": { + "description": "date on which an entity was created. This can be applied to nodes or edges", + "format": "date", + "type": "string" + }, "description": { "description": "a human-readable description of an entity", "type": "string" }, + "format": { + "type": "string" + }, "full_name": { "description": "a long-form human readable name for a thing", "type": "string" @@ -8236,21 +8219,13 @@ "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, - "in_taxon": { - "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", - "items": { - "type": "string" - }, - "type": "array" - }, - "in_taxon_label": { - "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" - }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, + "license": { + "type": "string" + }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" @@ -8262,6 +8237,16 @@ }, "type": "array" }, + "rights": { + "type": "string" + }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -8280,12 +8265,12 @@ "id", "category" ], - "title": "DiseaseOrPhenotypicFeature", + "title": "ConceptCountAnalysisResult", "type": "object" }, - "DiseaseOrPhenotypicFeatureExposure": { + "ConfidenceLevel": { "additionalProperties": false, - "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.", + "description": "Level of confidence in a statement", "properties": { "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -8295,10 +8280,18 @@ }, "type": "array" }, + "creation_date": { + "description": "date on which an entity was created. This can be applied to nodes or edges", + "format": "date", + "type": "string" + }, "description": { "description": "a human-readable description of an entity", "type": "string" }, + "format": { + "type": "string" + }, "full_name": { "description": "a long-form human readable name for a thing", "type": "string" @@ -8310,21 +8303,6 @@ }, "type": "array" }, - "has_attribute_type": { - "description": "connects an attribute to a class that describes it", - "type": "string" - }, - "has_qualitative_value": { - "description": "connects an attribute to a value", - "type": "string" - }, - "has_quantitative_value": { - "description": "connects an attribute to a value", - "items": { - "$ref": "#/$defs/QuantityValue" - }, - "type": "array" - }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" @@ -8333,8 +8311,11 @@ "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, + "license": { + "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.", + "description": "A human-readable name for an attribute or entity.", "type": "string" }, "provided_by": { @@ -8344,11 +8325,16 @@ }, "type": "array" }, - "timepoint": { - "description": "a point in time", - "format": "time", + "rights": { "type": "string" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -8364,22 +8350,15 @@ } }, "required": [ - "has_attribute_type", "id", "category" ], - "title": "DiseaseOrPhenotypicFeatureExposure", - "type": "object" - }, - "DiseaseOrPhenotypicFeatureOutcome": { - "additionalProperties": false, - "description": "Physiological outcomes resulting from an exposure event which is the manifestation of a disease or other characteristic phenotype.", - "title": "DiseaseOrPhenotypicFeatureOutcome", + "title": "ConfidenceLevel", "type": "object" }, - "DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation": { + "ContributorAssociation": { "additionalProperties": false, - "description": "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance.", + "description": "Any association between an entity (such as a publication) and various agents that contribute to its realisation", "properties": { "aggregator_knowledge_source": { "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", @@ -8434,7 +8413,7 @@ "type": "boolean" }, "object": { - "description": "genetic inheritance associated with the specified disease or phenotypic feature.", + "description": "agent helping to realise the given entity (e.g. such as a publication)", "type": "string" }, "object_category": { @@ -8479,7 +8458,7 @@ "type": "string" }, "predicate": { - "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", + "description": "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'", "type": "string" }, "primary_knowledge_source": { @@ -8494,7 +8473,7 @@ "type": "array" }, "qualifiers": { - "description": "connects an association to qualifiers that modify or qualify the meaning of that association", + "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" }, @@ -8508,7 +8487,7 @@ "type": "array" }, "subject": { - "description": "disease or phenotype", + "description": "information content entity which an agent has helped realise", "type": "string" }, "subject_category": { @@ -8559,12 +8538,12 @@ "object", "id" ], - "title": "DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", + "title": "ContributorAssociation", "type": "object" }, - "DiseaseOrPhenotypicFeatureToLocationAssociation": { + "CorrelatedGeneToDiseaseAssociation": { "additionalProperties": false, - "description": "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site.", + "description": "", "properties": { "aggregator_knowledge_source": { "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", @@ -8584,6 +8563,10 @@ "description": "a human-readable description of an entity", "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" + }, "has_attribute": { "description": "connects any entity to an attribute", "items": { @@ -8591,6 +8574,10 @@ }, "type": "array" }, + "has_count": { + "description": "number of things with a particular property", + "type": "integer" + }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { @@ -8598,6 +8585,17 @@ }, "type": "array" }, + "has_percentage": { + "description": "equivalent to has quotient multiplied by 100", + "type": "number" + }, + "has_quotient": { + "type": "number" + }, + "has_total": { + "description": "total number of things in a particular reference set", + "type": "integer" + }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" @@ -8619,7 +8617,7 @@ "type": "boolean" }, "object": { - "description": "anatomical entity in which the disease or feature is found.", + "description": "disease", "type": "string" }, "object_category": { @@ -8640,6 +8638,9 @@ }, "type": "array" }, + "object_direction_qualifier": { + "$ref": "#/$defs/DirectionQualifierEnum" + }, "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": { @@ -8651,6 +8652,10 @@ "description": "Used to 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" }, + "onset_qualifier": { + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "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" @@ -8692,10 +8697,21 @@ }, "type": "array" }, - "subject": { - "description": "disease or phenotype", + "severity_qualifier": { + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "type": "string" + }, + "sex_qualifier": { + "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string" }, + "subject": { + "$ref": "#/$defs/GeneOrGeneProduct", + "description": "gene in which variation is shown to correlate with the disease." + }, + "subject_aspect_qualifier": { + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum" + }, "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" @@ -8744,31 +8760,37 @@ "object", "id" ], - "title": "DiseaseOrPhenotypicFeatureToLocationAssociation", + "title": "CorrelatedGeneToDiseaseAssociation", "type": "object" }, - "DiseaseToExposureEventAssociation": { + "Dataset": { "additionalProperties": false, - "description": "An association between an exposure event and a disease.", + "description": "an item that refers to a collection of data from a data source.", "properties": { - "aggregator_knowledge_source": { - "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", - "items": { - "type": "string" - }, - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" }, + "creation_date": { + "description": "date on which an entity was created. This can be applied to nodes or edges", + "format": "date", + "type": "string" + }, "description": { "description": "a human-readable description of an entity", "type": "string" }, + "format": { + "type": "string" + }, + "full_name": { + "description": "a long-form human readable name for a thing", + "type": "string" + }, "has_attribute": { "description": "connects any entity to an attribute", "items": { @@ -8776,13 +8798,6 @@ }, "type": "array" }, - "has_evidence": { - "description": "connects an association to an instance of supporting evidence", - "items": { - "type": "string" - }, - "type": "array" - }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" @@ -8791,132 +8806,129 @@ "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "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.", + "license": { "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" }, - "negated": { - "description": "if set to true, then the association is negated i.e. is not true", - "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.", - "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" }, - "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.", + "rights": { "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.", + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, "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.", + "type": { "items": { "type": "string" }, "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.", + "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" + } + }, + "required": [ + "id", + "category" + ], + "title": "Dataset", + "type": "object" + }, + "DatasetDistribution": { + "additionalProperties": false, + "description": "an item that holds distribution level information about a dataset.", + "properties": { + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", + "type": "string" + }, + "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" - }, - "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.", + "creation_date": { + "description": "date on which an entity was created. This can be applied to nodes or edges", + "format": "date", "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.", + "description": { + "description": "a human-readable description of an entity", "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.", + "distribution_download_url": { "type": "string" }, - "predicate": { - "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", + "format": { "type": "string" }, - "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.", + "full_name": { + "description": "a long-form human readable name for a thing", "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.", + "has_attribute": { + "description": "connects any entity to an attribute", "items": { "type": "string" }, "type": "array" }, - "qualifiers": { - "description": "connects an association to qualifiers that modify or qualify the meaning of that association", - "items": { - "type": "string" - }, - "type": "array" + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "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" + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "type": "string" }, - "subject": { - "description": "disease class", + "license": { "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.", + "name": { + "description": "A human-readable name for an attribute or entity.", "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.", + "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" }, - "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.", + "rights": { + "type": "string" + }, + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, "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.", + "type": { "items": { "type": "string" }, "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" - }, - "timepoint": { - "description": "a point in time", - "format": "time", - "type": "string" - }, - "type": { - "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", + "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" }, @@ -8924,38 +8936,38 @@ } }, "required": [ - "subject", - "predicate", - "object", - "id" + "id", + "category" ], - "title": "DiseaseToExposureEventAssociation", + "title": "DatasetDistribution", "type": "object" }, - "DiseaseToPhenotypicFeatureAssociation": { + "DatasetSummary": { "additionalProperties": false, - "description": "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way.", + "description": "an item that holds summary level information about a dataset.", "properties": { - "aggregator_knowledge_source": { - "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", - "items": { - "type": "string" - }, - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" }, + "creation_date": { + "description": "date on which an entity was created. This can be applied to nodes or edges", + "format": "date", + "type": "string" + }, "description": { "description": "a human-readable description of an entity", "type": "string" }, - "frequency_qualifier": { - "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", + "format": { + "type": "string" + }, + "full_name": { + "description": "a long-form human readable name for a thing", "type": "string" }, "has_attribute": { @@ -8965,174 +8977,149 @@ }, "type": "array" }, - "has_count": { - "description": "number of things with a particular property", - "type": "integer" - }, - "has_evidence": { - "description": "connects an association to an instance of supporting evidence", - "items": { - "type": "string" - }, - "type": "array" - }, - "has_percentage": { - "description": "equivalent to has quotient multiplied by 100", - "type": "number" - }, - "has_quotient": { - "type": "number" - }, - "has_total": { - "description": "total number of things in a particular reference set", - "type": "integer" - }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", - "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" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "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.", + "license": { "type": "string" }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" }, - "negated": { - "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "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" }, - "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.", + "rights": { "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.", + "source_logo": { "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.", + "source_web_page": { + "type": "string" + }, + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, "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.", + "type": { "items": { "type": "string" }, "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.", + "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" + } + }, + "required": [ + "id", + "category" + ], + "title": "DatasetSummary", + "type": "object" + }, + "DatasetVersion": { + "additionalProperties": false, + "description": "an item that holds version level information about a dataset.", + "properties": { + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", + "type": "string" + }, + "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" - }, - "onset_qualifier": { - "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", - "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" - }, - "original_predicate": { - "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", + "creation_date": { + "description": "date on which an entity was created. This can be applied to nodes or edges", + "format": "date", "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.", + "description": { + "description": "a human-readable description of an entity", "type": "string" }, - "predicate": { - "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", + "format": { "type": "string" }, - "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.", + "full_name": { + "description": "a long-form human readable name for a thing", "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.", + "has_attribute": { + "description": "connects any entity to an attribute", "items": { "type": "string" }, "type": "array" }, - "qualifiers": { - "description": "connects an association to qualifiers that modify or qualify the meaning of that association", - "items": { - "type": "string" - }, - "type": "array" + "has_dataset": { + "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" + "has_distribution": { + "type": "string" }, - "severity_qualifier": { - "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, - "sex_qualifier": { - "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", + "ingest_date": { "type": "string" }, - "subject": { - "description": "disease class", + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", "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.", + "license": { "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.", + "name": { + "description": "A human-readable name for an attribute or entity.", + "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" }, - "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.", + "rights": { + "type": "string" + }, + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, "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.", + "type": { "items": { "type": "string" }, "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" - }, - "timepoint": { - "description": "a point in time", - "format": "time", - "type": "string" - }, - "type": { - "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", + "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" }, @@ -9140,25 +9127,16 @@ } }, "required": [ - "subject", - "predicate", - "object", - "id" + "id", + "category" ], - "title": "DiseaseToPhenotypicFeatureAssociation", + "title": "DatasetVersion", "type": "object" }, - "Drug": { + "Device": { "additionalProperties": false, - "description": "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease", + "description": "A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment", "properties": { - "available_from": { - "description": "", - "items": { - "$ref": "#/$defs/DrugAvailabilityEnum" - }, - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { @@ -9171,10 +9149,6 @@ "description": "a human-readable description of an entity", "type": "string" }, - "drug_regulatory_status_world_wide": { - "description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", - "type": "string" - }, "full_name": { "description": "a long-form human readable name for a thing", "type": "string" @@ -9186,17 +9160,6 @@ }, "type": "array" }, - "has_chemical_role": { - "description": "A role is particular behaviour which a chemical entity may exhibit.", - "items": { - "type": "string" - }, - "type": "array" - }, - "highest_FDA_approval_status": { - "description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", - "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" @@ -9205,18 +9168,6 @@ "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "is_supplement": { - "description": "", - "type": "string" - }, - "is_toxic": { - "description": "", - "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" - }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" @@ -9228,17 +9179,13 @@ }, "type": "array" }, - "routes_of_delivery": { - "description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { - "$ref": "#/$defs/DrugDeliveryEnum" + "type": "string" }, "type": "array" }, - "trade_name": { - "description": "", - "type": "string" - }, "type": { "items": { "type": "string" @@ -9257,32 +9204,12 @@ "id", "category" ], - "title": "Drug", + "title": "Device", "type": "object" }, - "DrugAvailabilityEnum": { - "description": "", - "enum": [ - "over_the_counter", - "prescription" - ], - "title": "DrugAvailabilityEnum", - "type": "string" - }, - "DrugDeliveryEnum": { - "description": "", - "enum": [ - "inhalation", - "oral", - "absorption_through_the_skin", - "intravenous_injection" - ], - "title": "DrugDeliveryEnum", - "type": "string" - }, - "DrugExposure": { + "DiagnosticAid": { "additionalProperties": false, - "description": "A drug exposure is an intake of a particular drug.", + "description": "A device or substance used to help diagnose disease or injury", "properties": { "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -9307,31 +9234,16 @@ }, "type": "array" }, - "has_attribute_type": { - "description": "connects an attribute to a class that describes it", + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, - "has_qualitative_value": { - "description": "connects an attribute to a value", - "type": "string" - }, - "has_quantitative_value": { - "description": "connects an attribute to a value", - "items": { - "$ref": "#/$defs/QuantityValue" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", - "type": "string" - }, - "iri": { - "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", "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.", + "description": "A human-readable name for an attribute or entity.", "type": "string" }, "provided_by": { @@ -9341,10 +9253,12 @@ }, "type": "array" }, - "timepoint": { - "description": "a point in time", - "format": "time", - "type": "string" + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" }, "type": { "items": { @@ -9361,24 +9275,37 @@ } }, "required": [ - "has_attribute_type", "id", "category" ], - "title": "DrugExposure", + "title": "DiagnosticAid", "type": "object" }, - "DrugLabel": { + "DigestType": { + "description": "", + "enum": [ + "SHA1", + "MD5", + "SHA256" + ], + "title": "DigestType", + "type": "string" + }, + "DirectionQualifierEnum": { + "description": "", + "enum": [ + "increased", + "upregulated", + "decreased", + "downregulated" + ], + "title": "DirectionQualifierEnum", + "type": "string" + }, + "Disease": { "additionalProperties": false, - "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.", + "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.", "properties": { - "authors": { - "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.", - "items": { - "type": "string" - }, - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { @@ -9387,18 +9314,10 @@ }, "type": "array" }, - "creation_date": { - "description": "date on which an entity was created. This can be applied to nodes or edges", - "format": "date", - "type": "string" - }, "description": { "description": "a human-readable description of an entity", "type": "string" }, - "format": { - "type": "string" - }, "full_name": { "description": "a long-form human readable name for a thing", "type": "string" @@ -9411,55 +9330,42 @@ "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.", - "type": "string" - }, - "iri": { - "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, - "keywords": { - "description": "keywords tagging a publication", + "in_taxon": { + "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": { "type": "string" }, "type": "array" }, - "license": { + "in_taxon_label": { + "description": "The human readable scientific name for the taxon of the entity.", "type": "string" }, - "mesh_terms": { - "description": "mesh terms tagging a publication", - "items": { - "type": "string" - }, - "type": "array" + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "type": "string" }, "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).", + "description": "A human-readable name for an attribute or entity.", "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.", + "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" }, - "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.", + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, "type": "array" }, - "rights": { - "type": "string" - }, - "summary": { - "description": "executive summary of a publication", - "type": "string" - }, "type": { "items": { "type": "string" @@ -9478,23 +9384,17 @@ "id", "category" ], - "title": "DrugLabel", + "title": "Disease", "type": "object" }, - "DrugToGeneAssociation": { + "DiseaseOrPhenotypicFeature": { "additionalProperties": false, - "description": "An interaction between a drug and a gene or gene product.", + "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.", "properties": { - "aggregator_knowledge_source": { - "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", - "items": { - "type": "string" - }, - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" @@ -9503,6 +9403,10 @@ "description": "a human-readable description of an entity", "type": "string" }, + "full_name": { + "description": "a long-form human readable name for a thing", + "type": "string" + }, "has_attribute": { "description": "connects any entity to an attribute", "items": { @@ -9510,236 +9414,138 @@ }, "type": "array" }, - "has_evidence": { - "description": "connects an association to an instance of supporting evidence", + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "in_taxon": { + "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": { "type": "string" }, "type": "array" }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "in_taxon_label": { + "description": "The human readable scientific name for the taxon of the entity.", "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "knowledge_source": { - "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" - }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" }, - "negated": { - "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" - }, - "object": { - "$ref": "#/$defs/GeneOrGeneProduct", - "description": "the gene or gene product that is affected by the drug" - }, - "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" - }, - "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.", + "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" }, - "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.", + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, "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.", + "type": { "items": { "type": "string" }, "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" + "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" + } + }, + "required": [ + "id", + "category" + ], + "title": "DiseaseOrPhenotypicFeature", + "type": "object" + }, + "DiseaseOrPhenotypicFeatureExposure": { + "additionalProperties": false, + "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.", + "properties": { + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", + "type": "string" + }, + "type": "array" }, - "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.", + "description": { + "description": "a human-readable description of an entity", "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.", + "full_name": { + "description": "a long-form human readable name for a thing", "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" + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" }, - "predicate": { - "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", + "has_attribute_type": { + "description": "connects an attribute to a class that describes it", "type": "string" }, - "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.", + "has_qualitative_value": { + "description": "connects an attribute to a value", "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.", + "has_quantitative_value": { + "description": "connects an attribute to a value", "items": { - "type": "string" + "$ref": "#/$defs/QuantityValue" }, "type": "array" }, - "qualifiers": { - "description": "connects an association to qualifiers that modify or qualify the meaning of that association", + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "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" + }, + "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" }, - "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.", + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, "type": "array" }, - "subject": { - "description": "the drug that is an interactor", - "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.", + "timepoint": { + "description": "a point in time", + "format": "time", "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" - }, - "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" - }, - "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" - }, - "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" - }, - "timepoint": { - "description": "a point in time", - "format": "time", - "type": "string" - }, - "type": { - "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "required": [ - "subject", - "predicate", - "object", - "id" - ], - "title": "DrugToGeneAssociation", - "type": "object" - }, - "DrugToGeneInteractionExposure": { - "additionalProperties": false, - "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.", - "properties": { - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", - "items": { - "pattern": "^biolink:[A-Z][A-Za-z]+$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of an entity", - "type": "string" - }, - "full_name": { - "description": "a long-form human readable name for a thing", - "type": "string" - }, - "has_attribute": { - "description": "connects any entity to an attribute", - "items": { - "type": "string" - }, - "type": "array" - }, - "has_attribute_type": { - "description": "connects an attribute to a class that describes it", - "type": "string" - }, - "has_gene_or_gene_product": { - "description": "connects an entity with one or more gene or gene products", - "items": { - "type": "string" - }, - "type": "array" - }, - "has_qualitative_value": { - "description": "connects an attribute to a value", - "type": "string" - }, - "has_quantitative_value": { - "description": "connects an attribute to a value", - "items": { - "$ref": "#/$defs/QuantityValue" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", - "type": "string" - }, - "iri": { - "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "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" - }, - "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" - }, - "timepoint": { - "description": "a point in time", - "format": "time", - "type": "string" - }, - "type": { + "type": { "items": { "type": "string" }, @@ -9758,23 +9564,18 @@ "id", "category" ], - "title": "DrugToGeneInteractionExposure", + "title": "DiseaseOrPhenotypicFeatureExposure", "type": "object" }, - "DruggableGeneCategoryEnum": { - "description": "", - "enum": [ - "tclin", - "tbio", - "tchem", - "tdark" - ], - "title": "DruggableGeneCategoryEnum", - "type": "string" + "DiseaseOrPhenotypicFeatureOutcome": { + "additionalProperties": false, + "description": "Physiological outcomes resulting from an exposure event which is the manifestation of a disease or other characteristic phenotype.", + "title": "DiseaseOrPhenotypicFeatureOutcome", + "type": "object" }, - "DruggableGeneToDiseaseAssociation": { + "DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation": { "additionalProperties": false, - "description": "", + "description": "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance.", "properties": { "aggregator_knowledge_source": { "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", @@ -9794,10 +9595,6 @@ "description": "a human-readable description of an entity", "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" - }, "has_attribute": { "description": "connects any entity to an attribute", "items": { @@ -9805,28 +9602,13 @@ }, "type": "array" }, - "has_count": { - "description": "number of things with a particular property", - "type": "integer" - }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { - "$ref": "#/$defs/DruggableGeneCategoryEnum" + "type": "string" }, "type": "array" }, - "has_percentage": { - "description": "equivalent to has quotient multiplied by 100", - "type": "number" - }, - "has_quotient": { - "type": "number" - }, - "has_total": { - "description": "total number of things in a particular reference set", - "type": "integer" - }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" @@ -9848,7 +9630,7 @@ "type": "boolean" }, "object": { - "description": "disease", + "description": "genetic inheritance associated with the specified disease or phenotypic feature.", "type": "string" }, "object_category": { @@ -9869,9 +9651,6 @@ }, "type": "array" }, - "object_direction_qualifier": { - "$ref": "#/$defs/DirectionQualifierEnum" - }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { @@ -9883,10 +9662,6 @@ "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string" }, - "onset_qualifier": { - "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", - "type": "string" - }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string" @@ -9928,20 +9703,9 @@ }, "type": "array" }, - "severity_qualifier": { - "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", - "type": "string" - }, - "sex_qualifier": { - "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" - }, "subject": { - "$ref": "#/$defs/GeneOrGeneProduct", - "description": "gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state." - }, - "subject_aspect_qualifier": { - "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum" + "description": "disease or phenotype", + "type": "string" }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -9991,17 +9755,13 @@ "object", "id" ], - "title": "DruggableGeneToDiseaseAssociation", + "title": "DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation", "type": "object" }, - "EntityToDiseaseAssociation": { + "DiseaseOrPhenotypicFeatureToLocationAssociation": { "additionalProperties": false, - "description": "", + "description": "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site.", "properties": { - "FDA_approval_status": { - "$ref": "#/$defs/FDAApprovalStatusEnum", - "description": "" - }, "aggregator_knowledge_source": { "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": { @@ -10055,7 +9815,7 @@ "type": "boolean" }, "object": { - "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", + "description": "anatomical entity in which the disease or feature is found.", "type": "string" }, "object_category": { @@ -10129,7 +9889,7 @@ "type": "array" }, "subject": { - "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", + "description": "disease or phenotype", "type": "string" }, "subject_category": { @@ -10180,17 +9940,13 @@ "object", "id" ], - "title": "EntityToDiseaseAssociation", + "title": "DiseaseOrPhenotypicFeatureToLocationAssociation", "type": "object" }, - "EntityToPhenotypicFeatureAssociation": { + "DiseaseToExposureEventAssociation": { "additionalProperties": false, - "description": "", + "description": "An association between an exposure event and a disease.", "properties": { - "FDA_approval_status": { - "$ref": "#/$defs/FDAApprovalStatusEnum", - "description": "" - }, "aggregator_knowledge_source": { "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": { @@ -10318,7 +10074,7 @@ "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.", + "description": "disease class", "type": "string" }, "subject_category": { @@ -10369,17 +10125,23 @@ "object", "id" ], - "title": "EntityToPhenotypicFeatureAssociation", + "title": "DiseaseToExposureEventAssociation", "type": "object" }, - "EnvironmentalExposure": { + "DiseaseToPhenotypicFeatureAssociation": { "additionalProperties": false, - "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.", + "description": "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way.", "properties": { + "aggregator_knowledge_source": { + "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", + "items": { + "type": "string" + }, + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { - "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" @@ -10388,8 +10150,8 @@ "description": "a human-readable description of an entity", "type": "string" }, - "full_name": { - "description": "a long-form human readable name for a thing", + "frequency_qualifier": { + "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string" }, "has_attribute": { @@ -10399,21 +10161,28 @@ }, "type": "array" }, - "has_attribute_type": { - "description": "connects an attribute to a class that describes it", - "type": "string" - }, - "has_qualitative_value": { - "description": "connects an attribute to a value", - "type": "string" + "has_count": { + "description": "number of things with a particular property", + "type": "integer" }, - "has_quantitative_value": { - "description": "connects an attribute to a value", + "has_evidence": { + "description": "connects an association to an instance of supporting evidence", "items": { - "$ref": "#/$defs/QuantityValue" + "type": "string" }, "type": "array" }, + "has_percentage": { + "description": "equivalent to has quotient multiplied by 100", + "type": "number" + }, + "has_quotient": { + "type": "number" + }, + "has_total": { + "description": "total number of things in a particular reference set", + "type": "integer" + }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" @@ -10422,30 +10191,144 @@ "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, + "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" + }, "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.", + "description": "A human-readable name for an attribute or entity.", "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.", + "negated": { + "description": "if set to true, then the association is negated i.e. is not true", + "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.", + "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" + }, + "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" }, - "timepoint": { - "description": "a point in time", - "format": "time", + "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" + }, + "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" + }, + "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" }, - "type": { + "onset_qualifier": { + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "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" + }, + "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" + }, + "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" + }, + "predicate": { + "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", + "type": "string" + }, + "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" + }, + "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" }, - "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.", + "qualifiers": { + "description": "connects an association to qualifiers that modify or qualify the meaning of that association", + "items": { + "type": "string" + }, + "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" + }, + "severity_qualifier": { + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "type": "string" + }, + "sex_qualifier": { + "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", + "type": "string" + }, + "subject": { + "description": "disease class", + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "timepoint": { + "description": "a point in time", + "format": "time", + "type": "string" + }, + "type": { + "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, @@ -10453,31 +10336,33 @@ } }, "required": [ - "has_attribute_type", - "id", - "category" + "subject", + "predicate", + "object", + "id" ], - "title": "EnvironmentalExposure", + "title": "DiseaseToPhenotypicFeatureAssociation", "type": "object" }, - "EnvironmentalFeature": { + "DissociatedCellSample": { "additionalProperties": false, "description": "", "properties": { "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { - "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" }, + "cell_prep_type": { + "type": "string" + }, "description": { "description": "a human-readable description of an entity", "type": "string" }, - "full_name": { - "description": "a long-form human readable name for a thing", + "facs_population_plan": { "type": "string" }, "has_attribute": { @@ -10499,45 +10384,60 @@ "description": "A human-readable name for an attribute or entity.", "type": "string" }, - "provided_by": { - "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", + "num_cells_collected": { + "type": "integer" + }, + "type": { "items": { "type": "string" }, "type": "array" }, - "type": { + "wasAttributedTo": { "items": { - "type": "string" + "$ref": "#/$defs/Agent" }, "type": "array" }, - "xref": { - "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", + "wasDerivedFrom": { "items": { - "type": "string" + "$ref": "#/$defs/TissueSample" + }, + "type": "array" + }, + "wasGeneratedBy": { + "items": { + "$ref": "#/$defs/CellDissociation" }, "type": "array" } }, "required": [ - "id", - "category" + "id" ], - "title": "EnvironmentalFeature", + "title": "DissociatedCellSample", "type": "object" }, - "EnvironmentalFoodContaminant": { + "Donor": { "additionalProperties": false, - "description": "", + "description": "A person or organism that is the source of a biological sample.", "properties": { - "available_from": { - "description": "", + "address": { + "description": "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?).", + "type": "string" + }, + "affiliation": { + "description": "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations.", "items": { - "$ref": "#/$defs/DrugAvailabilityEnum" + "type": "string" }, "type": "array" }, + "birth_date": { + "description": "The date of birth of the donor.", + "format": "date", + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { @@ -10546,10 +10446,23 @@ }, "type": "array" }, + "death_age": { + "description": "The age of the donor at the time of death (ISO 8601 format).", + "type": "string" + }, + "death_date": { + "description": "The date of death of the donor.", + "format": "date", + "type": "string" + }, "description": { "description": "a human-readable description of an entity", "type": "string" }, + "full_genotype": { + "description": "The full genotype of the donor.", + "type": "string" + }, "full_name": { "description": "a long-form human readable name for a thing", "type": "string" @@ -10561,31 +10474,27 @@ }, "type": "array" }, - "has_chemical_role": { - "description": "A role is particular behaviour which a chemical entity may exhibit.", + "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.", + "type": "string" + }, + "in_taxon": { + "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": { "type": "string" }, "type": "array" }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "in_taxon_label": { + "description": "The human readable scientific name for the taxon of the entity.", "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "is_toxic": { - "description": "", - "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" - }, "name": { - "description": "A human-readable name for an attribute or entity.", + "description": "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"", "type": "string" }, "provided_by": { @@ -10595,9 +10504,15 @@ }, "type": "array" }, - "trade_name": { - "description": "", - "type": "string" + "sex": { + "$ref": "#/$defs/SexType" + }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" }, "type": { "items": { @@ -10617,13 +10532,20 @@ "id", "category" ], - "title": "EnvironmentalFoodContaminant", + "title": "Donor", "type": "object" }, - "EnvironmentalProcess": { + "Drug": { "additionalProperties": false, - "description": "", + "description": "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease", "properties": { + "available_from": { + "description": "", + "items": { + "$ref": "#/$defs/DrugAvailabilityEnum" + }, + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { @@ -10636,6 +10558,10 @@ "description": "a human-readable description of an entity", "type": "string" }, + "drug_regulatory_status_world_wide": { + "description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", + "type": "string" + }, "full_name": { "description": "a long-form human readable name for a thing", "type": "string" @@ -10647,6 +10573,17 @@ }, "type": "array" }, + "has_chemical_role": { + "description": "A role is particular behaviour which a chemical entity may exhibit.", + "items": { + "type": "string" + }, + "type": "array" + }, + "highest_FDA_approval_status": { + "description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", + "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" @@ -10655,16 +10592,46 @@ "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "name": { - "description": "A human-readable name for an attribute or entity.", + "is_supplement": { + "description": "", "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" + "is_toxic": { + "description": "", + "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" + }, + "name": { + "description": "A human-readable name for an attribute or entity.", + "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" + }, + "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" + }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, + "trade_name": { + "description": "", + "type": "string" }, "type": { "items": { @@ -10684,18 +10651,32 @@ "id", "category" ], - "title": "EnvironmentalProcess", + "title": "Drug", "type": "object" }, - "EpidemiologicalOutcome": { - "additionalProperties": false, - "description": "An epidemiological outcome, such as societal disease burden, resulting from an exposure event.", - "title": "EpidemiologicalOutcome", - "type": "object" + "DrugAvailabilityEnum": { + "description": "", + "enum": [ + "over_the_counter", + "prescription" + ], + "title": "DrugAvailabilityEnum", + "type": "string" }, - "Event": { + "DrugDeliveryEnum": { + "description": "", + "enum": [ + "inhalation", + "oral", + "absorption_through_the_skin", + "intravenous_injection" + ], + "title": "DrugDeliveryEnum", + "type": "string" + }, + "DrugExposure": { "additionalProperties": false, - "description": "Something that happens at a given place and time.", + "description": "A drug exposure is an intake of a particular drug.", "properties": { "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -10720,6 +10701,21 @@ }, "type": "array" }, + "has_attribute_type": { + "description": "connects an attribute to a class that describes it", + "type": "string" + }, + "has_qualitative_value": { + "description": "connects an attribute to a value", + "type": "string" + }, + "has_quantitative_value": { + "description": "connects an attribute to a value", + "items": { + "$ref": "#/$defs/QuantityValue" + }, + "type": "array" + }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" @@ -10729,7 +10725,7 @@ "type": "string" }, "name": { - "description": "A human-readable name for an attribute or entity.", + "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" }, "provided_by": { @@ -10739,6 +10735,18 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, + "timepoint": { + "description": "a point in time", + "format": "time", + "type": "string" + }, "type": { "items": { "type": "string" @@ -10754,16 +10762,24 @@ } }, "required": [ + "has_attribute_type", "id", "category" ], - "title": "Event", + "title": "DrugExposure", "type": "object" }, - "EvidenceType": { + "DrugLabel": { "additionalProperties": false, - "description": "Class of evidence that supports an association", + "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.", "properties": { + "authors": { + "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.", + "items": { + "type": "string" + }, + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { @@ -10795,6 +10811,120 @@ }, "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.", + "type": "string" + }, + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "type": "string" + }, + "keywords": { + "description": "keywords tagging a publication", + "items": { + "type": "string" + }, + "type": "array" + }, + "license": { + "type": "string" + }, + "mesh_terms": { + "description": "mesh terms tagging a publication", + "items": { + "type": "string" + }, + "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" + }, + "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" + }, + "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" + }, + "rights": { + "type": "string" + }, + "summary": { + "description": "executive summary of a publication", + "type": "string" + }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, + "type": { + "items": { + "type": "string" + }, + "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" + } + }, + "required": [ + "id", + "category" + ], + "title": "DrugLabel", + "type": "object" + }, + "DrugToGeneAssociation": { + "additionalProperties": false, + "description": "An interaction between a drug and a gene or gene product.", + "properties": { + "aggregator_knowledge_source": { + "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", + "items": { + "type": "string" + }, + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_evidence": { + "description": "connects an association to an instance of supporting evidence", + "items": { + "type": "string" + }, + "type": "array" + }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" @@ -10803,31 +10933,2135 @@ "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "license": { + "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" + }, + "name": { + "description": "A human-readable name for an attribute or entity.", + "type": "string" + }, + "negated": { + "description": "if set to true, then the association is negated i.e. is not true", + "type": "boolean" + }, + "object": { + "$ref": "#/$defs/GeneOrGeneProduct", + "description": "the gene or gene product that is affected by the drug" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "predicate": { + "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", + "type": "string" + }, + "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" + }, + "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" + }, + "qualifiers": { + "description": "connects an association to qualifiers that modify or qualify the meaning of that association", + "items": { + "type": "string" + }, + "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" + }, + "subject": { + "description": "the drug that is an interactor", + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "timepoint": { + "description": "a point in time", + "format": "time", + "type": "string" + }, + "type": { + "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", + "items": { + "type": "string" + }, + "type": "array" + } + }, + "required": [ + "subject", + "predicate", + "object", + "id" + ], + "title": "DrugToGeneAssociation", + "type": "object" + }, + "DrugToGeneInteractionExposure": { + "additionalProperties": false, + "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.", + "properties": { + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "full_name": { + "description": "a long-form human readable name for a thing", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_attribute_type": { + "description": "connects an attribute to a class that describes it", + "type": "string" + }, + "has_gene_or_gene_product": { + "description": "connects an entity with one or more gene or gene products", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_qualitative_value": { + "description": "connects an attribute to a value", + "type": "string" + }, + "has_quantitative_value": { + "description": "connects an attribute to a value", + "items": { + "$ref": "#/$defs/QuantityValue" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "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" + }, + "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" + }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, + "timepoint": { + "description": "a point in time", + "format": "time", + "type": "string" + }, + "type": { + "items": { + "type": "string" + }, + "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" + } + }, + "required": [ + "has_attribute_type", + "id", + "category" + ], + "title": "DrugToGeneInteractionExposure", + "type": "object" + }, + "DruggableGeneCategoryEnum": { + "description": "", + "enum": [ + "tclin", + "tbio", + "tchem", + "tdark" + ], + "title": "DruggableGeneCategoryEnum", + "type": "string" + }, + "DruggableGeneToDiseaseAssociation": { + "additionalProperties": false, + "description": "", + "properties": { + "aggregator_knowledge_source": { + "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", + "items": { + "type": "string" + }, + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "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" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_count": { + "description": "number of things with a particular property", + "type": "integer" + }, + "has_evidence": { + "description": "connects an association to an instance of supporting evidence", + "items": { + "$ref": "#/$defs/DruggableGeneCategoryEnum" + }, + "type": "array" + }, + "has_percentage": { + "description": "equivalent to has quotient multiplied by 100", + "type": "number" + }, + "has_quotient": { + "type": "number" + }, + "has_total": { + "description": "total number of things in a particular reference set", + "type": "integer" + }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "type": "string" + }, + "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" + }, + "name": { + "description": "A human-readable name for an attribute or entity.", + "type": "string" + }, + "negated": { + "description": "if set to true, then the association is negated i.e. is not true", + "type": "boolean" + }, + "object": { + "description": "disease", + "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" + }, + "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" + }, + "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" + }, + "object_direction_qualifier": { + "$ref": "#/$defs/DirectionQualifierEnum" + }, + "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" + }, + "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" + }, + "onset_qualifier": { + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "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" + }, + "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" + }, + "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" + }, + "predicate": { + "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", + "type": "string" + }, + "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" + }, + "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" + }, + "qualifiers": { + "description": "connects an association to qualifiers that modify or qualify the meaning of that association", + "items": { + "type": "string" + }, + "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" + }, + "severity_qualifier": { + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "type": "string" + }, + "sex_qualifier": { + "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", + "type": "string" + }, + "subject": { + "$ref": "#/$defs/GeneOrGeneProduct", + "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." + }, + "subject_aspect_qualifier": { + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "timepoint": { + "description": "a point in time", + "format": "time", + "type": "string" + }, + "type": { + "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", + "items": { + "type": "string" + }, + "type": "array" + } + }, + "required": [ + "subject", + "predicate", + "object", + "id" + ], + "title": "DruggableGeneToDiseaseAssociation", + "type": "object" + }, + "EnrichedCellSample": { + "additionalProperties": false, + "description": "", + "properties": { + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "type": "string" + }, + "name": { + "description": "A human-readable name for an attribute or entity.", + "type": "string" + }, + "type": { + "items": { + "type": "string" + }, + "type": "array" + }, + "wasAttributedTo": { + "items": { + "$ref": "#/$defs/Agent" + }, + "type": "array" + }, + "wasDerivedFrom": { + "items": { + "$ref": "#/$defs/DissociatedCellSample" + }, + "type": "array" + }, + "wasGeneratedBy": { + "items": { + "$ref": "#/$defs/CellEnrichment" + }, + "type": "array" + } + }, + "required": [ + "id" + ], + "title": "EnrichedCellSample", + "type": "object" + }, + "EntityToDiseaseAssociation": { + "additionalProperties": false, + "description": "", + "properties": { + "FDA_approval_status": { + "$ref": "#/$defs/FDAApprovalStatusEnum", + "description": "" + }, + "aggregator_knowledge_source": { + "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", + "items": { + "type": "string" + }, + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_evidence": { + "description": "connects an association to an instance of supporting evidence", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "type": "string" + }, + "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" + }, + "name": { + "description": "A human-readable name for an attribute or entity.", + "type": "string" + }, + "negated": { + "description": "if set to true, then the association is negated i.e. is not true", + "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.", + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "predicate": { + "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", + "type": "string" + }, + "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" + }, + "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" + }, + "qualifiers": { + "description": "connects an association to qualifiers that modify or qualify the meaning of that association", + "items": { + "type": "string" + }, + "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" + }, + "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.", + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "timepoint": { + "description": "a point in time", + "format": "time", + "type": "string" + }, + "type": { + "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", + "items": { + "type": "string" + }, + "type": "array" + } + }, + "required": [ + "subject", + "predicate", + "object", + "id" + ], + "title": "EntityToDiseaseAssociation", + "type": "object" + }, + "EntityToPhenotypicFeatureAssociation": { + "additionalProperties": false, + "description": "", + "properties": { + "FDA_approval_status": { + "$ref": "#/$defs/FDAApprovalStatusEnum", + "description": "" + }, + "aggregator_knowledge_source": { + "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", + "items": { + "type": "string" + }, + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_evidence": { + "description": "connects an association to an instance of supporting evidence", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "type": "string" + }, + "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" + }, + "name": { + "description": "A human-readable name for an attribute or entity.", + "type": "string" + }, + "negated": { + "description": "if set to true, then the association is negated i.e. is not true", + "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.", + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "predicate": { + "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", + "type": "string" + }, + "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" + }, + "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" + }, + "qualifiers": { + "description": "connects an association to qualifiers that modify or qualify the meaning of that association", + "items": { + "type": "string" + }, + "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" + }, + "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.", + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "timepoint": { + "description": "a point in time", + "format": "time", + "type": "string" + }, + "type": { + "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", + "items": { + "type": "string" + }, + "type": "array" + } + }, + "required": [ + "subject", + "predicate", + "object", + "id" + ], + "title": "EntityToPhenotypicFeatureAssociation", + "type": "object" + }, + "EnvironmentalExposure": { + "additionalProperties": false, + "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.", + "properties": { + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "full_name": { + "description": "a long-form human readable name for a thing", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_attribute_type": { + "description": "connects an attribute to a class that describes it", + "type": "string" + }, + "has_qualitative_value": { + "description": "connects an attribute to a value", + "type": "string" + }, + "has_quantitative_value": { + "description": "connects an attribute to a value", + "items": { + "$ref": "#/$defs/QuantityValue" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "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" + }, + "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" + }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, + "timepoint": { + "description": "a point in time", + "format": "time", + "type": "string" + }, + "type": { + "items": { + "type": "string" + }, + "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" + } + }, + "required": [ + "has_attribute_type", + "id", + "category" + ], + "title": "EnvironmentalExposure", + "type": "object" + }, + "EnvironmentalFeature": { + "additionalProperties": false, + "description": "", + "properties": { + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "full_name": { + "description": "a long-form human readable name for a thing", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "type": "string" + }, + "name": { + "description": "A human-readable name for an attribute or entity.", + "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" + }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, + "type": { + "items": { + "type": "string" + }, + "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" + } + }, + "required": [ + "id", + "category" + ], + "title": "EnvironmentalFeature", + "type": "object" + }, + "EnvironmentalFoodContaminant": { + "additionalProperties": false, + "description": "", + "properties": { + "available_from": { + "description": "", + "items": { + "$ref": "#/$defs/DrugAvailabilityEnum" + }, + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "full_name": { + "description": "a long-form human readable name for a thing", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_chemical_role": { + "description": "A role is particular behaviour which a chemical entity may exhibit.", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "type": "string" + }, + "is_toxic": { + "description": "", + "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" + }, + "name": { + "description": "A human-readable name for an attribute or entity.", + "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" + }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, + "trade_name": { + "description": "", + "type": "string" + }, + "type": { + "items": { + "type": "string" + }, + "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" + } + }, + "required": [ + "id", + "category" + ], + "title": "EnvironmentalFoodContaminant", + "type": "object" + }, + "EnvironmentalProcess": { + "additionalProperties": false, + "description": "", + "properties": { + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "full_name": { + "description": "a long-form human readable name for a thing", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "type": "string" + }, + "name": { + "description": "A human-readable name for an attribute or entity.", + "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" + }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, + "type": { + "items": { + "type": "string" + }, + "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" + } + }, + "required": [ + "id", + "category" + ], + "title": "EnvironmentalProcess", + "type": "object" + }, + "EpidemiologicalOutcome": { + "additionalProperties": false, + "description": "An epidemiological outcome, such as societal disease burden, resulting from an exposure event.", + "title": "EpidemiologicalOutcome", + "type": "object" + }, + "Event": { + "additionalProperties": false, + "description": "Something that happens at a given place and time.", + "properties": { + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "full_name": { + "description": "a long-form human readable name for a thing", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "type": "string" + }, + "name": { + "description": "A human-readable name for an attribute or entity.", + "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" + }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, + "type": { + "items": { + "type": "string" + }, + "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" + } + }, + "required": [ + "id", + "category" + ], + "title": "Event", + "type": "object" + }, + "EvidenceType": { + "additionalProperties": false, + "description": "Class of evidence that supports an association", + "properties": { + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", + "type": "string" + }, + "type": "array" + }, + "creation_date": { + "description": "date on which an entity was created. This can be applied to nodes or edges", + "format": "date", + "type": "string" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "format": { + "type": "string" + }, + "full_name": { + "description": "a long-form human readable name for a thing", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "type": "string" + }, + "license": { + "type": "string" + }, + "name": { + "description": "A human-readable name for an attribute or entity.", + "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" + }, + "rights": { + "type": "string" + }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, + "type": { + "items": { + "type": "string" + }, + "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" + } + }, + "required": [ + "id", + "category" + ], + "title": "EvidenceType", + "type": "object" + }, + "Exon": { + "additionalProperties": false, + "description": "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing.", + "properties": { + "available_from": { + "description": "", + "items": { + "$ref": "#/$defs/DrugAvailabilityEnum" + }, + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "full_name": { + "description": "a long-form human readable name for a thing", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_biological_sequence": { + "description": "connects a genomic feature to its sequence", + "type": "string" + }, + "has_chemical_role": { + "description": "A role is particular behaviour which a chemical entity may exhibit.", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "in_taxon": { + "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", + "items": { + "type": "string" + }, + "type": "array" + }, + "in_taxon_label": { + "description": "The human readable scientific name for the taxon of the entity.", + "type": "string" + }, + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "type": "string" + }, + "is_metabolite": { + "description": "indicates whether a molecular entity is a metabolite", + "type": "boolean" + }, + "is_toxic": { + "description": "", + "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" + }, + "name": { + "description": "A human-readable name for an attribute or entity.", + "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" + }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, + "trade_name": { + "description": "", + "type": "string" + }, + "type": { + "items": { + "type": "string" + }, + "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" + } + }, + "required": [ + "id", + "category" + ], + "title": "Exon", + "type": "object" + }, + "ExonToTranscriptRelationship": { + "additionalProperties": false, + "description": "A transcript is formed from multiple exons", + "properties": { + "aggregator_knowledge_source": { + "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", + "items": { + "type": "string" + }, + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_evidence": { + "description": "connects an association to an instance of supporting evidence", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "type": "string" + }, + "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" + }, + "name": { + "description": "A human-readable name for an attribute or entity.", + "type": "string" + }, + "negated": { + "description": "if set to true, then the association is negated i.e. is not true", + "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.", + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "predicate": { + "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", + "type": "string" + }, + "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" + }, + "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" + }, + "qualifiers": { + "description": "connects an association to qualifiers that modify or qualify the meaning of that association", + "items": { + "type": "string" + }, + "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" + }, + "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.", + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "timepoint": { + "description": "a point in time", + "format": "time", + "type": "string" + }, + "type": { + "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", + "items": { + "type": "string" + }, + "type": "array" + } + }, + "required": [ + "subject", + "predicate", + "object", + "id" + ], + "title": "ExonToTranscriptRelationship", + "type": "object" + }, + "ExposureEventToOutcomeAssociation": { + "additionalProperties": false, + "description": "An association between an exposure event and an outcome.", + "properties": { + "aggregator_knowledge_source": { + "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", + "items": { + "type": "string" + }, + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_evidence": { + "description": "connects an association to an instance of supporting evidence", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "type": "string" + }, + "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" + }, + "name": { + "description": "A human-readable name for an attribute or entity.", + "type": "string" + }, + "negated": { + "description": "if set to true, then the association is negated i.e. is not true", + "type": "boolean" + }, + "object": { + "$ref": "#/$defs/Outcome", + "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "population_context_qualifier": { + "description": "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association.", + "type": "string" + }, + "predicate": { + "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", + "type": "string" + }, + "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" + }, + "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" + }, + "qualifiers": { + "description": "connects an association to qualifiers that modify or qualify the meaning of that association", + "items": { + "type": "string" + }, + "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" + }, + "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.", + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "timepoint": { + "description": "a point in time", + "format": "time", + "type": "string" + }, + "type": { + "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", + "items": { + "type": "string" + }, + "type": "array" + } + }, + "required": [ + "subject", + "predicate", + "object", + "id" + ], + "title": "ExposureEventToOutcomeAssociation", + "type": "object" + }, + "ExposureEventToPhenotypicFeatureAssociation": { + "additionalProperties": false, + "description": "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype.", + "properties": { + "aggregator_knowledge_source": { + "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", + "items": { + "type": "string" + }, + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "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" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_count": { + "description": "number of things with a particular property", + "type": "integer" + }, + "has_evidence": { + "description": "connects an association to an instance of supporting evidence", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_percentage": { + "description": "equivalent to has quotient multiplied by 100", + "type": "number" + }, + "has_quotient": { + "type": "number" + }, + "has_total": { + "description": "total number of things in a particular reference set", + "type": "integer" + }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "type": "string" + }, + "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" + }, + "name": { + "description": "A human-readable name for an attribute or entity.", + "type": "string" + }, + "negated": { + "description": "if set to true, then the association is negated i.e. is not true", + "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.", + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "onset_qualifier": { + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "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" + }, + "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" + }, + "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" + }, + "predicate": { + "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", + "type": "string" + }, + "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" + }, + "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" + }, + "qualifiers": { + "description": "connects an association to qualifiers that modify or qualify the meaning of that association", + "items": { + "type": "string" + }, + "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" + }, + "severity_qualifier": { + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "type": "string" + }, + "sex_qualifier": { + "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", + "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.", "type": "string" }, - "name": { - "description": "A human-readable name for an attribute or entity.", + "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" }, - "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.", + "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" }, - "rights": { - "type": "string" + "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" }, - "type": { + "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" }, - "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.", + "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" + }, + "timepoint": { + "description": "a point in time", + "format": "time", + "type": "string" + }, + "type": { + "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, @@ -10835,15 +13069,50 @@ } }, "required": [ - "id", - "category" + "subject", + "predicate", + "object", + "id" ], - "title": "EvidenceType", + "title": "ExposureEventToPhenotypicFeatureAssociation", "type": "object" }, - "Exon": { + "FDAApprovalStatusEnum": { + "description": "", + "enum": [ + "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" + ], + "title": "FDAApprovalStatusEnum", + "type": "string" + }, + "FDAIDAAdverseEventEnum": { + "description": "please consult with the FDA guidelines as proposed in this document: https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/cfrsearch.cfm?fr=312.32", + "enum": [ + "life_threatening_adverse_event", + "serious_adverse_event", + "suspected_adverse_reaction", + "unexpected_adverse_event" + ], + "title": "FDAIDAAdverseEventEnum", + "type": "string" + }, + "Food": { "additionalProperties": false, - "description": "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing.", + "description": "A substance consumed by a living organism as a source of nutrition", "properties": { "available_from": { "description": "", @@ -10864,6 +13133,10 @@ "description": "a human-readable description of an entity", "type": "string" }, + "drug_regulatory_status_world_wide": { + "description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", + "type": "string" + }, "full_name": { "description": "a long-form human readable name for a thing", "type": "string" @@ -10875,10 +13148,6 @@ }, "type": "array" }, - "has_biological_sequence": { - "description": "connects a genomic feature to its sequence", - "type": "string" - }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { @@ -10886,28 +13155,21 @@ }, "type": "array" }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "highest_FDA_approval_status": { + "description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", "type": "string" }, - "in_taxon": { - "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", - "items": { - "type": "string" - }, - "type": "array" - }, - "in_taxon_label": { - "description": "The human readable scientific name for the taxon of the entity.", + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "is_metabolite": { - "description": "indicates whether a molecular entity is a metabolite", - "type": "boolean" + "is_supplement": { + "description": "", + "type": "string" }, "is_toxic": { "description": "", @@ -10928,6 +13190,20 @@ }, "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": "#/$defs/DrugDeliveryEnum" + }, + "type": "array" + }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "trade_name": { "description": "", "type": "string" @@ -10950,23 +13226,24 @@ "id", "category" ], - "title": "Exon", + "title": "Food", "type": "object" }, - "ExonToTranscriptRelationship": { + "FoodAdditive": { "additionalProperties": false, - "description": "A transcript is formed from multiple exons", + "description": "", "properties": { - "aggregator_knowledge_source": { - "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", + "available_from": { + "description": "", "items": { - "type": "string" + "$ref": "#/$defs/DrugAvailabilityEnum" }, "type": "array" }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" @@ -10975,6 +13252,10 @@ "description": "a human-readable description of an entity", "type": "string" }, + "full_name": { + "description": "a long-form human readable name for a thing", + "type": "string" + }, "has_attribute": { "description": "connects any entity to an attribute", "items": { @@ -10982,8 +13263,8 @@ }, "type": "array" }, - "has_evidence": { - "description": "connects an association to an instance of supporting evidence", + "has_chemical_role": { + "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, @@ -10997,132 +13278,44 @@ "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "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" - }, - "name": { - "description": "A human-readable name for an attribute or entity.", - "type": "string" - }, - "negated": { - "description": "if set to true, then the association is negated i.e. is not true", + "is_toxic": { + "description": "", "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.", - "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" - }, - "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" - }, - "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" - }, - "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" - }, - "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" - }, - "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" - }, - "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" - }, - "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" - }, - "predicate": { - "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", - "type": "string" - }, - "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" - }, - "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" - }, - "qualifiers": { - "description": "connects an association to qualifiers that modify or qualify the meaning of that association", - "items": { - "type": "string" - }, - "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" - }, - "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.", + "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" }, - "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.", + "name": { + "description": "A human-readable name for an attribute or entity.", "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" - }, - "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.", + "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" }, - "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.", + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, "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" - }, - "timepoint": { - "description": "a point in time", - "format": "time", + "trade_name": { + "description": "", "type": "string" }, "type": { - "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", + "items": { + "type": "string" + }, + "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" }, @@ -11130,17 +13323,15 @@ } }, "required": [ - "subject", - "predicate", - "object", - "id" + "id", + "category" ], - "title": "ExonToTranscriptRelationship", + "title": "FoodAdditive", "type": "object" }, - "ExposureEventToOutcomeAssociation": { + "FunctionalAssociation": { "additionalProperties": false, - "description": "An association between an exposure event and an outcome.", + "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.", "properties": { "aggregator_knowledge_source": { "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", @@ -11195,8 +13386,8 @@ "type": "boolean" }, "object": { - "$ref": "#/$defs/Outcome", - "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." + "description": "class describing the activity, process or localization of the gene product", + "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.", @@ -11239,10 +13430,6 @@ "description": "used 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" }, - "population_context_qualifier": { - "description": "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association.", - "type": "string" - }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string" @@ -11273,8 +13460,8 @@ "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.", - "type": "string" + "$ref": "#/$defs/MacromolecularMachineMixin", + "description": "gene, product or macromolecular complex that has the function associated with the GO term" }, "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.", @@ -11305,11 +13492,6 @@ "description": "Used to 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" }, - "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" - }, "timepoint": { "description": "a point in time", "format": "time", @@ -11329,23 +13511,17 @@ "object", "id" ], - "title": "ExposureEventToOutcomeAssociation", + "title": "FunctionalAssociation", "type": "object" }, - "ExposureEventToPhenotypicFeatureAssociation": { + "Fungus": { "additionalProperties": false, - "description": "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype.", + "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).", "properties": { - "aggregator_knowledge_source": { - "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", - "items": { - "type": "string" - }, - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" @@ -11354,185 +13530,62 @@ "description": "a human-readable description of an entity", "type": "string" }, - "frequency_qualifier": { - "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", + "full_name": { + "description": "a long-form human readable name for a thing", "type": "string" }, "has_attribute": { - "description": "connects any entity to an attribute", + "description": "may often be an organism attribute", "items": { "type": "string" }, "type": "array" }, - "has_count": { - "description": "number of things with a particular property", - "type": "integer" + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" }, - "has_evidence": { - "description": "connects an association to an instance of supporting evidence", + "in_taxon": { + "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": { "type": "string" }, "type": "array" }, - "has_percentage": { - "description": "equivalent to has quotient multiplied by 100", - "type": "number" - }, - "has_quotient": { - "type": "number" - }, - "has_total": { - "description": "total number of things in a particular reference set", - "type": "integer" - }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "in_taxon_label": { + "description": "The human readable scientific name for the taxon of the entity.", "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "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" - }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" }, - "negated": { - "description": "if set to true, then the association is negated i.e. is not true", - "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.", - "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" - }, - "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" - }, - "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" - }, - "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" - }, - "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" - }, - "onset_qualifier": { - "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", - "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" - }, - "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" - }, - "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" - }, - "predicate": { - "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", - "type": "string" - }, - "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" - }, - "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" - }, - "qualifiers": { - "description": "connects an association to qualifiers that modify or qualify the meaning of that association", - "items": { - "type": "string" - }, - "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" - }, - "severity_qualifier": { - "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", - "type": "string" - }, - "sex_qualifier": { - "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "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.", - "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" - }, - "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.", + "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" }, - "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.", + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, "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.", + "type": { "items": { "type": "string" }, "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" - }, - "timepoint": { - "description": "a point in time", - "format": "time", - "type": "string" - }, - "type": { - "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", + "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" }, @@ -11540,58 +13593,16 @@ } }, "required": [ - "subject", - "predicate", - "object", - "id" - ], - "title": "ExposureEventToPhenotypicFeatureAssociation", - "type": "object" - }, - "FDAApprovalStatusEnum": { - "description": "", - "enum": [ - "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" - ], - "title": "FDAApprovalStatusEnum", - "type": "string" - }, - "FDAIDAAdverseEventEnum": { - "description": "please consult with the FDA guidelines as proposed in this document: https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/cfrsearch.cfm?fr=312.32", - "enum": [ - "life_threatening_adverse_event", - "serious_adverse_event", - "suspected_adverse_reaction", - "unexpected_adverse_event" + "id", + "category" ], - "title": "FDAIDAAdverseEventEnum", - "type": "string" + "title": "Fungus", + "type": "object" }, - "Food": { + "Gene": { "additionalProperties": false, - "description": "A substance consumed by a living organism as a source of nutrition", + "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.", "properties": { - "available_from": { - "description": "", - "items": { - "$ref": "#/$defs/DrugAvailabilityEnum" - }, - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { @@ -11604,10 +13615,6 @@ "description": "a human-readable description of an entity", "type": "string" }, - "drug_regulatory_status_world_wide": { - "description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.", - "type": "string" - }, "full_name": { "description": "a long-form human readable name for a thing", "type": "string" @@ -11619,39 +13626,31 @@ }, "type": "array" }, - "has_chemical_role": { - "description": "A role is particular behaviour which a chemical entity may exhibit.", - "items": { - "type": "string" - }, - "type": "array" - }, - "highest_FDA_approval_status": { - "description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'FDA approval status.'", + "has_biological_sequence": { + "description": "connects a genomic feature to its sequence", "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" }, - "iri": { - "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "in_taxon": { + "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", + "items": { + "type": "string" + }, + "type": "array" }, - "is_supplement": { - "description": "", + "in_taxon_label": { + "description": "The human readable scientific name for the taxon of the entity.", "type": "string" }, - "is_toxic": { - "description": "", - "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.", + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, "name": { - "description": "A human-readable name for an attribute or entity.", + "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" }, "provided_by": { @@ -11661,17 +13660,17 @@ }, "type": "array" }, - "routes_of_delivery": { - "description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", + "symbol": { + "description": "Symbol for a particular thing", + "type": "string" + }, + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { - "$ref": "#/$defs/DrugDeliveryEnum" + "type": "string" }, "type": "array" }, - "trade_name": { - "description": "", - "type": "string" - }, "type": { "items": { "type": "string" @@ -11690,20 +13689,13 @@ "id", "category" ], - "title": "Food", + "title": "Gene", "type": "object" }, - "FoodAdditive": { + "GeneAnnotation": { "additionalProperties": false, - "description": "", + "description": "An annotation describing the location, boundaries, and functions of individual genes within a genome annotation.", "properties": { - "available_from": { - "description": "", - "items": { - "$ref": "#/$defs/DrugAvailabilityEnum" - }, - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { @@ -11727,31 +13719,34 @@ }, "type": "array" }, - "has_chemical_role": { - "description": "A role is particular behaviour which a chemical entity may exhibit.", + "has_biological_sequence": { + "description": "connects a genomic feature to its sequence", + "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" + }, + "in_taxon": { + "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": { "type": "string" }, "type": "array" }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "in_taxon_label": { + "description": "The human readable scientific name for the taxon of the entity.", "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "is_toxic": { - "description": "", - "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" + "molecular_type": { + "$ref": "#/$defs/BioType" }, "name": { - "description": "A human-readable name for an attribute or entity.", + "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" }, "provided_by": { @@ -11761,10 +13756,24 @@ }, "type": "array" }, - "trade_name": { - "description": "", + "referenced_in": { + "type": "string" + }, + "source_id": { + "description": "The authority specific identifier.", + "type": "string" + }, + "symbol": { + "description": "Symbol for a particular thing", "type": "string" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -11783,12 +13792,12 @@ "id", "category" ], - "title": "FoodAdditive", + "title": "GeneAnnotation", "type": "object" }, - "FunctionalAssociation": { + "GeneAsAModelOfDiseaseAssociation": { "additionalProperties": false, - "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.", + "description": "", "properties": { "aggregator_knowledge_source": { "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", @@ -11808,6 +13817,10 @@ "description": "a human-readable description of an entity", "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" + }, "has_attribute": { "description": "connects any entity to an attribute", "items": { @@ -11815,6 +13828,10 @@ }, "type": "array" }, + "has_count": { + "description": "number of things with a particular property", + "type": "integer" + }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { @@ -11822,6 +13839,17 @@ }, "type": "array" }, + "has_percentage": { + "description": "equivalent to has quotient multiplied by 100", + "type": "number" + }, + "has_quotient": { + "type": "number" + }, + "has_total": { + "description": "total number of things in a particular reference set", + "type": "integer" + }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" @@ -11843,7 +13871,7 @@ "type": "boolean" }, "object": { - "description": "class describing the activity, process or localization of the gene product", + "description": "disease", "type": "string" }, "object_category": { @@ -11864,6 +13892,9 @@ }, "type": "array" }, + "object_direction_qualifier": { + "$ref": "#/$defs/DirectionQualifierEnum" + }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { @@ -11875,6 +13906,10 @@ "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string" }, + "onset_qualifier": { + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "type": "string" + }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string" @@ -11888,7 +13923,7 @@ "type": "string" }, "predicate": { - "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", + "description": "The relationship to the disease", "type": "string" }, "primary_knowledge_source": { @@ -11916,9 +13951,20 @@ }, "type": "array" }, + "severity_qualifier": { + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "type": "string" + }, + "sex_qualifier": { + "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", + "type": "string" + }, "subject": { - "$ref": "#/$defs/MacromolecularMachineMixin", - "description": "gene, product or macromolecular complex that has the function associated with the GO term" + "$ref": "#/$defs/GeneOrGeneProduct", + "description": "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." + }, + "subject_aspect_qualifier": { + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum" }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", @@ -11963,95 +14009,17 @@ } }, "required": [ - "subject", - "predicate", - "object", - "id" - ], - "title": "FunctionalAssociation", - "type": "object" - }, - "Fungus": { - "additionalProperties": false, - "description": "A kingdom of eukaryotic, heterotrophic organisms that live as saprobes or parasites, including mushrooms, yeasts, smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi refer to those that grow as multicellular colonies (mushrooms and molds).", - "properties": { - "category": { - "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", - "items": { - "pattern": "^biolink:[A-Z][A-Za-z]+$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of an entity", - "type": "string" - }, - "full_name": { - "description": "a long-form human readable name for a thing", - "type": "string" - }, - "has_attribute": { - "description": "may often be an organism attribute", - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", - "type": "string" - }, - "in_taxon": { - "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", - "items": { - "type": "string" - }, - "type": "array" - }, - "in_taxon_label": { - "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" - }, - "iri": { - "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" - }, - "name": { - "description": "A human-readable name for an attribute or entity.", - "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" - }, - "type": { - "items": { - "type": "string" - }, - "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" - } - }, - "required": [ - "id", - "category" + "subject", + "predicate", + "object", + "id" ], - "title": "Fungus", + "title": "GeneAsAModelOfDiseaseAssociation", "type": "object" }, - "Gene": { + "GeneFamily": { "additionalProperties": false, - "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.", + "description": "any grouping of multiple genes or gene products related by common descent", "properties": { "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -12076,9 +14044,12 @@ }, "type": "array" }, - "has_biological_sequence": { - "description": "connects a genomic feature to its sequence", - "type": "string" + "has_gene_or_gene_product": { + "description": "connects an entity with one or more gene or gene products", + "items": { + "type": "string" + }, + "type": "array" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -12100,7 +14071,7 @@ "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", + "description": "A human-readable name for an attribute or entity.", "type": "string" }, "provided_by": { @@ -12110,10 +14081,6 @@ }, "type": "array" }, - "symbol": { - "description": "Symbol for a particular thing", - "type": "string" - }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { @@ -12139,17 +14106,23 @@ "id", "category" ], - "title": "Gene", + "title": "GeneFamily", "type": "object" }, - "GeneAnnotation": { + "GeneHasVariantThatContributesToDiseaseAssociation": { "additionalProperties": false, - "description": "An annotation describing the location, boundaries, and functions of individual genes within a genome annotation.", + "description": "", "properties": { + "aggregator_knowledge_source": { + "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", + "items": { + "type": "string" + }, + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { - "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" @@ -12158,8 +14131,8 @@ "description": "a human-readable description of an entity", "type": "string" }, - "full_name": { - "description": "a long-form human readable name for a thing", + "frequency_qualifier": { + "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string" }, "has_attribute": { @@ -12169,69 +14142,183 @@ }, "type": "array" }, - "has_biological_sequence": { - "description": "connects a genomic feature to its sequence", - "type": "string" + "has_count": { + "description": "number of things with a particular property", + "type": "integer" + }, + "has_evidence": { + "description": "connects an association to an instance of supporting evidence", + "items": { + "type": "string" + }, + "type": "array" + }, + "has_percentage": { + "description": "equivalent to has quotient multiplied by 100", + "type": "number" + }, + "has_quotient": { + "type": "number" + }, + "has_total": { + "description": "total number of things in a particular reference set", + "type": "integer" }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, - "in_taxon": { - "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "type": "string" + }, + "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" + }, + "name": { + "description": "A human-readable name for an attribute or entity.", + "type": "string" + }, + "negated": { + "description": "if set to true, then the association is negated i.e. is not true", + "type": "boolean" + }, + "object": { + "description": "disease", + "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" + }, + "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" }, - "in_taxon_label": { - "description": "The human readable scientific name for the taxon of the entity.", + "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" + }, + "object_direction_qualifier": { + "$ref": "#/$defs/DirectionQualifierEnum" + }, + "object_label_closure": { + "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", + "items": { + "type": "string" + }, + "type": "array" + }, + "object_namespace": { + "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string" }, - "iri": { - "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "onset_qualifier": { + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string" }, - "molecular_type": { - "$ref": "#/$defs/BioType" + "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" }, - "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", + "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" }, - "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.", + "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" + }, + "predicate": { + "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", + "type": "string" + }, + "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" + }, + "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" }, - "referenced_in": { + "qualifiers": { + "description": "connects an association to qualifiers that modify or qualify the meaning of that association", + "items": { + "type": "string" + }, + "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" + }, + "severity_qualifier": { + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string" }, - "source_id": { - "description": "The authority specific identifier.", + "sex_qualifier": { + "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string" }, - "symbol": { - "description": "Symbol for a particular thing", + "subject": { + "$ref": "#/$defs/GeneOrGeneProduct", + "description": "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." + }, + "subject_aspect_qualifier": { + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum" + }, + "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" }, - "synonym": { - "description": "Alternate human-readable names for a thing", + "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" }, - "type": { + "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" }, - "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.", + "subject_form_or_variant_qualifier": { + "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" + }, + "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" + }, + "timepoint": { + "description": "a point in time", + "format": "time", + "type": "string" + }, + "type": { + "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, @@ -12239,13 +14326,86 @@ } }, "required": [ - "id", - "category" + "subject", + "predicate", + "object", + "id" + ], + "title": "GeneHasVariantThatContributesToDiseaseAssociation", + "type": "object" + }, + "GeneOrGeneProductOrChemicalEntityAspectEnum": { + "description": "", + "enum": [ + "activity_or_abundance", + "abundance", + "activity", + "expression", + "synthesis", + "degradation", + "cleavage", + "hydrolysis", + "metabolic_processing", + "mutation_rate", + "stability", + "folding", + "localization", + "transport", + "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" ], - "title": "GeneAnnotation", - "type": "object" + "title": "GeneOrGeneProductOrChemicalEntityAspectEnum", + "type": "string" }, - "GeneAsAModelOfDiseaseAssociation": { + "GeneOrGeneProductOrChemicalPartQualifierEnum": { + "description": "", + "enum": [ + "3_prime_utr", + "5_prime_utr", + "polya_tail", + "promoter", + "enhancer", + "exon", + "intron" + ], + "title": "GeneOrGeneProductOrChemicalPartQualifierEnum", + "type": "string" + }, + "GeneToDiseaseAssociation": { "additionalProperties": false, "description": "", "properties": { @@ -12373,7 +14533,7 @@ "type": "string" }, "predicate": { - "description": "The relationship to the disease", + "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string" }, "primary_knowledge_source": { @@ -12411,7 +14571,7 @@ }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", - "description": "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." + "description": "gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model" }, "subject_aspect_qualifier": { "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum" @@ -12464,17 +14624,23 @@ "object", "id" ], - "title": "GeneAsAModelOfDiseaseAssociation", + "title": "GeneToDiseaseAssociation", "type": "object" }, - "GeneFamily": { + "GeneToDiseaseOrPhenotypicFeatureAssociation": { "additionalProperties": false, - "description": "any grouping of multiple genes or gene products related by common descent", + "description": "", "properties": { + "aggregator_knowledge_source": { + "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", + "items": { + "type": "string" + }, + "type": "array" + }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { - "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" @@ -12483,8 +14649,8 @@ "description": "a human-readable description of an entity", "type": "string" }, - "full_name": { - "description": "a long-form human readable name for a thing", + "frequency_qualifier": { + "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string" }, "has_attribute": { @@ -12494,51 +14660,180 @@ }, "type": "array" }, - "has_gene_or_gene_product": { - "description": "connects an entity with one or more gene or gene products", + "has_count": { + "description": "number of things with a particular property", + "type": "integer" + }, + "has_evidence": { + "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, "type": "array" }, + "has_percentage": { + "description": "equivalent to has quotient multiplied by 100", + "type": "number" + }, + "has_quotient": { + "type": "number" + }, + "has_total": { + "description": "total number of things in a particular reference set", + "type": "integer" + }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, - "in_taxon": { - "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "type": "string" + }, + "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" + }, + "name": { + "description": "A human-readable name for an attribute or entity.", + "type": "string" + }, + "negated": { + "description": "if set to true, then the association is negated i.e. is not true", + "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.", + "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" + }, + "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" }, - "in_taxon_label": { - "description": "The human readable scientific name for the taxon of the entity.", + "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" + }, + "object_direction_qualifier": { + "$ref": "#/$defs/DirectionQualifierEnum" + }, + "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" + }, + "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" }, - "iri": { - "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "onset_qualifier": { + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string" }, - "name": { - "description": "A human-readable name for an attribute or entity.", + "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" }, - "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.", + "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" + }, + "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" + }, + "predicate": { + "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", + "type": "string" + }, + "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" + }, + "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" }, - "type": { + "qualifiers": { + "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, "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.", + "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" + }, + "severity_qualifier": { + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "type": "string" + }, + "sex_qualifier": { + "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", + "type": "string" + }, + "subject": { + "$ref": "#/$defs/GeneOrGeneProduct", + "description": "gene in which variation is correlated with the phenotypic feature" + }, + "subject_aspect_qualifier": { + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "timepoint": { + "description": "a point in time", + "format": "time", + "type": "string" + }, + "type": { + "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, @@ -12546,15 +14841,17 @@ } }, "required": [ - "id", - "category" + "subject", + "predicate", + "object", + "id" ], - "title": "GeneFamily", + "title": "GeneToDiseaseOrPhenotypicFeatureAssociation", "type": "object" }, - "GeneHasVariantThatContributesToDiseaseAssociation": { + "GeneToExpressionSiteAssociation": { "additionalProperties": false, - "description": "", + "description": "An association between a gene and a gene expression site, possibly qualified by stage/timing info.", "properties": { "aggregator_knowledge_source": { "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", @@ -12574,10 +14871,6 @@ "description": "a human-readable description of an entity", "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" - }, "has_attribute": { "description": "connects any entity to an attribute", "items": { @@ -12585,10 +14878,6 @@ }, "type": "array" }, - "has_count": { - "description": "number of things with a particular property", - "type": "integer" - }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { @@ -12596,17 +14885,6 @@ }, "type": "array" }, - "has_percentage": { - "description": "equivalent to has quotient multiplied by 100", - "type": "number" - }, - "has_quotient": { - "type": "number" - }, - "has_total": { - "description": "total number of things in a particular reference set", - "type": "integer" - }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" @@ -12628,7 +14906,7 @@ "type": "boolean" }, "object": { - "description": "disease", + "description": "location in which the gene is expressed", "type": "string" }, "object_category": { @@ -12649,9 +14927,6 @@ }, "type": "array" }, - "object_direction_qualifier": { - "$ref": "#/$defs/DirectionQualifierEnum" - }, "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": { @@ -12663,10 +14938,6 @@ "description": "Used to 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" }, - "onset_qualifier": { - "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", - "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" @@ -12680,7 +14951,7 @@ "type": "string" }, "predicate": { - "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", + "description": "expression relationship", "type": "string" }, "primary_knowledge_source": { @@ -12701,6 +14972,10 @@ }, "type": "array" }, + "quantifier_qualifier": { + "description": "can be used to indicate magnitude, or also ranking", + "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": { @@ -12708,20 +14983,13 @@ }, "type": "array" }, - "severity_qualifier": { - "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", - "type": "string" - }, - "sex_qualifier": { - "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", + "stage_qualifier": { + "description": "stage at which the gene is expressed in the site", "type": "string" }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", - "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." - }, - "subject_aspect_qualifier": { - "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum" + "description": "Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location." }, "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.", @@ -12741,9 +15009,6 @@ }, "type": "array" }, - "subject_form_or_variant_qualifier": { - "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": { @@ -12774,81 +15039,12 @@ "object", "id" ], - "title": "GeneHasVariantThatContributesToDiseaseAssociation", + "title": "GeneToExpressionSiteAssociation", "type": "object" }, - "GeneOrGeneProductOrChemicalEntityAspectEnum": { - "description": "", - "enum": [ - "activity_or_abundance", - "abundance", - "activity", - "expression", - "synthesis", - "degradation", - "cleavage", - "hydrolysis", - "metabolic_processing", - "mutation_rate", - "stability", - "folding", - "localization", - "transport", - "secretion", - "uptake", - "molecular_modification", - "acetylation", - "acylation", - "alkylation", - "amination", - "carbamoylation", - "ethylation", - "glutathionylation", - "glycation", - "glycosylation", - "glucuronidation", - "n_linked_glycosylation", - "o_linked_glycosylation", - "hydroxylation", - "lipidation", - "farnesylation", - "geranoylation", - "myristoylation", - "palmitoylation", - "prenylation", - "methylation", - "nitrosation", - "nucleotidylation", - "phosphorylation", - "ribosylation", - "ADP-ribosylation", - "sulfation", - "sumoylation", - "ubiquitination", - "oxidation", - "reduction", - "carboxylation" - ], - "title": "GeneOrGeneProductOrChemicalEntityAspectEnum", - "type": "string" - }, - "GeneOrGeneProductOrChemicalPartQualifierEnum": { - "description": "", - "enum": [ - "3_prime_utr", - "5_prime_utr", - "polya_tail", - "promoter", - "enhancer", - "exon", - "intron" - ], - "title": "GeneOrGeneProductOrChemicalPartQualifierEnum", - "type": "string" - }, - "GeneToDiseaseAssociation": { + "GeneToGeneCoexpressionAssociation": { "additionalProperties": false, - "description": "", + "description": "Indicates that two genes are co-expressed, generally under the same conditions.", "properties": { "aggregator_knowledge_source": { "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", @@ -12868,8 +15064,8 @@ "description": "a human-readable description of an entity", "type": "string" }, - "frequency_qualifier": { - "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", + "expression_site": { + "description": "location in which gene or protein expression takes place. May be cell, tissue, or organ.", "type": "string" }, "has_attribute": { @@ -12879,10 +15075,6 @@ }, "type": "array" }, - "has_count": { - "description": "number of things with a particular property", - "type": "integer" - }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { @@ -12890,17 +15082,6 @@ }, "type": "array" }, - "has_percentage": { - "description": "equivalent to has quotient multiplied by 100", - "type": "number" - }, - "has_quotient": { - "type": "number" - }, - "has_total": { - "description": "total number of things in a particular reference set", - "type": "integer" - }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" @@ -12922,8 +15103,8 @@ "type": "boolean" }, "object": { - "description": "disease", - "type": "string" + "$ref": "#/$defs/GeneOrGeneProduct", + "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." }, "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.", @@ -12943,9 +15124,6 @@ }, "type": "array" }, - "object_direction_qualifier": { - "$ref": "#/$defs/DirectionQualifierEnum" - }, "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": { @@ -12957,10 +15135,6 @@ "description": "Used to 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" }, - "onset_qualifier": { - "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", - "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" @@ -12973,6 +15147,10 @@ "description": "used 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" }, + "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" + }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string" @@ -12995,6 +15173,10 @@ }, "type": "array" }, + "quantifier_qualifier": { + "description": "Optional quantitative value indicating degree of expression.", + "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": { @@ -13002,20 +15184,13 @@ }, "type": "array" }, - "severity_qualifier": { - "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", - "type": "string" - }, - "sex_qualifier": { - "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", + "stage_qualifier": { + "description": "stage during which gene or protein expression of takes place.", "type": "string" }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", - "description": "gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model" - }, - "subject_aspect_qualifier": { - "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum" + "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." }, "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.", @@ -13065,12 +15240,12 @@ "object", "id" ], - "title": "GeneToDiseaseAssociation", + "title": "GeneToGeneCoexpressionAssociation", "type": "object" }, - "GeneToDiseaseOrPhenotypicFeatureAssociation": { + "GeneToGeneFamilyAssociation": { "additionalProperties": false, - "description": "", + "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.", "properties": { "aggregator_knowledge_source": { "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", @@ -13090,10 +15265,6 @@ "description": "a human-readable description of an entity", "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" - }, "has_attribute": { "description": "connects any entity to an attribute", "items": { @@ -13101,10 +15272,6 @@ }, "type": "array" }, - "has_count": { - "description": "number of things with a particular property", - "type": "integer" - }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { @@ -13112,17 +15279,6 @@ }, "type": "array" }, - "has_percentage": { - "description": "equivalent to has quotient multiplied by 100", - "type": "number" - }, - "has_quotient": { - "type": "number" - }, - "has_total": { - "description": "total number of things in a particular reference set", - "type": "integer" - }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" @@ -13165,9 +15321,6 @@ }, "type": "array" }, - "object_direction_qualifier": { - "$ref": "#/$defs/DirectionQualifierEnum" - }, "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": { @@ -13179,10 +15332,6 @@ "description": "Used to 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" }, - "onset_qualifier": { - "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", - "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" @@ -13196,7 +15345,7 @@ "type": "string" }, "predicate": { - "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", + "description": "membership of the gene in the given gene family.", "type": "string" }, "primary_knowledge_source": { @@ -13224,20 +15373,9 @@ }, "type": "array" }, - "severity_qualifier": { - "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", - "type": "string" - }, - "sex_qualifier": { - "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" - }, "subject": { - "$ref": "#/$defs/GeneOrGeneProduct", - "description": "gene in which variation is correlated with the phenotypic feature" - }, - "subject_aspect_qualifier": { - "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum" + "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.", + "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.", @@ -13287,12 +15425,12 @@ "object", "id" ], - "title": "GeneToDiseaseOrPhenotypicFeatureAssociation", + "title": "GeneToGeneFamilyAssociation", "type": "object" }, - "GeneToExpressionSiteAssociation": { + "GeneToGeneHomologyAssociation": { "additionalProperties": false, - "description": "An association between a gene and a gene expression site, possibly qualified by stage/timing info.", + "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)", "properties": { "aggregator_knowledge_source": { "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", @@ -13347,8 +15485,8 @@ "type": "boolean" }, "object": { - "description": "location in which the gene is expressed", - "type": "string" + "$ref": "#/$defs/GeneOrGeneProduct", + "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." }, "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.", @@ -13392,7 +15530,7 @@ "type": "string" }, "predicate": { - "description": "expression relationship", + "description": "homology relationship type", "type": "string" }, "primary_knowledge_source": { @@ -13413,10 +15551,6 @@ }, "type": "array" }, - "quantifier_qualifier": { - "description": "can be used to indicate magnitude, or also ranking", - "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": { @@ -13424,13 +15558,9 @@ }, "type": "array" }, - "stage_qualifier": { - "description": "stage at which the gene is expressed in the site", - "type": "string" - }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", - "description": "Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location." + "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." }, "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.", @@ -13480,12 +15610,12 @@ "object", "id" ], - "title": "GeneToExpressionSiteAssociation", + "title": "GeneToGeneHomologyAssociation", "type": "object" }, - "GeneToGeneCoexpressionAssociation": { + "GeneToGeneProductRelationship": { "additionalProperties": false, - "description": "Indicates that two genes are co-expressed, generally under the same conditions.", + "description": "A gene is transcribed and potentially translated to a gene product", "properties": { "aggregator_knowledge_source": { "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", @@ -13505,10 +15635,6 @@ "description": "a human-readable description of an entity", "type": "string" }, - "expression_site": { - "description": "location in which gene or protein expression takes place. May be cell, tissue, or organ.", - "type": "string" - }, "has_attribute": { "description": "connects any entity to an attribute", "items": { @@ -13544,8 +15670,8 @@ "type": "boolean" }, "object": { - "$ref": "#/$defs/GeneOrGeneProduct", - "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." + "$ref": "#/$defs/GeneProductMixin", + "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." }, "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.", @@ -13588,10 +15714,6 @@ "description": "used 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" }, - "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" - }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string" @@ -13614,10 +15736,6 @@ }, "type": "array" }, - "quantifier_qualifier": { - "description": "Optional quantitative value indicating degree of expression.", - "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": { @@ -13625,13 +15743,9 @@ }, "type": "array" }, - "stage_qualifier": { - "description": "stage during which gene or protein expression of takes place.", - "type": "string" - }, "subject": { - "$ref": "#/$defs/GeneOrGeneProduct", - "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." + "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.", + "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.", @@ -13681,12 +15795,12 @@ "object", "id" ], - "title": "GeneToGeneCoexpressionAssociation", + "title": "GeneToGeneProductRelationship", "type": "object" }, - "GeneToGeneFamilyAssociation": { + "GeneToGoTermAssociation": { "additionalProperties": false, - "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.", + "description": "", "properties": { "aggregator_knowledge_source": { "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", @@ -13741,7 +15855,7 @@ "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.", + "description": "class describing the activity, process or localization of the gene product", "type": "string" }, "object_category": { @@ -13786,7 +15900,7 @@ "type": "string" }, "predicate": { - "description": "membership of the gene in the given gene family.", + "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string" }, "primary_knowledge_source": { @@ -13815,7 +15929,7 @@ "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.", + "description": "gene, product or macromolecular complex that has the function associated with the GO term", "type": "string" }, "subject_category": { @@ -13866,12 +15980,12 @@ "object", "id" ], - "title": "GeneToGeneFamilyAssociation", + "title": "GeneToGoTermAssociation", "type": "object" }, - "GeneToGeneHomologyAssociation": { + "GeneToPathwayAssociation": { "additionalProperties": false, - "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)", + "description": "An interaction between a gene or gene product and a biological process or pathway.", "properties": { "aggregator_knowledge_source": { "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", @@ -13926,8 +16040,8 @@ "type": "boolean" }, "object": { - "$ref": "#/$defs/GeneOrGeneProduct", - "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." + "description": "the pathway that includes or is affected by the gene or gene product", + "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.", @@ -13971,7 +16085,7 @@ "type": "string" }, "predicate": { - "description": "homology relationship type", + "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string" }, "primary_knowledge_source": { @@ -14001,7 +16115,7 @@ }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", - "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." + "description": "the gene or gene product entity that participates or influences the pathway" }, "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.", @@ -14051,12 +16165,12 @@ "object", "id" ], - "title": "GeneToGeneHomologyAssociation", + "title": "GeneToPathwayAssociation", "type": "object" }, - "GeneToGeneProductRelationship": { + "GeneToPhenotypicFeatureAssociation": { "additionalProperties": false, - "description": "A gene is transcribed and potentially translated to a gene product", + "description": "", "properties": { "aggregator_knowledge_source": { "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", @@ -14076,6 +16190,10 @@ "description": "a human-readable description of an entity", "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" + }, "has_attribute": { "description": "connects any entity to an attribute", "items": { @@ -14083,6 +16201,10 @@ }, "type": "array" }, + "has_count": { + "description": "number of things with a particular property", + "type": "integer" + }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { @@ -14090,6 +16212,17 @@ }, "type": "array" }, + "has_percentage": { + "description": "equivalent to has quotient multiplied by 100", + "type": "number" + }, + "has_quotient": { + "type": "number" + }, + "has_total": { + "description": "total number of things in a particular reference set", + "type": "integer" + }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" @@ -14111,8 +16244,8 @@ "type": "boolean" }, "object": { - "$ref": "#/$defs/GeneProductMixin", - "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is 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.", + "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.", @@ -14132,6 +16265,9 @@ }, "type": "array" }, + "object_direction_qualifier": { + "$ref": "#/$defs/DirectionQualifierEnum" + }, "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": { @@ -14143,6 +16279,10 @@ "description": "Used to 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" }, + "onset_qualifier": { + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "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" @@ -14184,10 +16324,21 @@ }, "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.", + "severity_qualifier": { + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "type": "string" + }, + "sex_qualifier": { + "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", "type": "string" }, + "subject": { + "$ref": "#/$defs/GeneOrGeneProduct", + "description": "gene in which variation is correlated with the phenotypic feature" + }, + "subject_aspect_qualifier": { + "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum" + }, "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" @@ -14236,23 +16387,17 @@ "object", "id" ], - "title": "GeneToGeneProductRelationship", + "title": "GeneToPhenotypicFeatureAssociation", "type": "object" }, - "GeneToGoTermAssociation": { + "GeneticInheritance": { "additionalProperties": false, - "description": "", + "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.", "properties": { - "aggregator_knowledge_source": { - "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", - "items": { - "type": "string" - }, - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" @@ -14261,6 +16406,10 @@ "description": "a human-readable description of an entity", "type": "string" }, + "full_name": { + "description": "a long-form human readable name for a thing", + "type": "string" + }, "has_attribute": { "description": "connects any entity to an attribute", "items": { @@ -14268,147 +16417,252 @@ }, "type": "array" }, - "has_evidence": { - "description": "connects an association to an instance of supporting evidence", + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "in_taxon": { + "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": { "type": "string" }, "type": "array" }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "in_taxon_label": { + "description": "The human readable scientific name for the taxon of the entity.", "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "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" - }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" }, - "negated": { - "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" - }, - "object": { - "description": "class describing the activity, process or localization of the gene product", - "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" }, - "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" + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" }, - "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.", + "type": { "items": { "type": "string" }, "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.", + "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" + } + }, + "required": [ + "id", + "category" + ], + "title": "GeneticInheritance", + "type": "object" + }, + "Genome": { + "additionalProperties": false, + "description": "A genome is the sum of genetic material within a cell or virion.", + "properties": { + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "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.", + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "full_name": { + "description": "a long-form human readable name for a thing", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", "items": { "type": "string" }, "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.", + "has_biological_sequence": { + "description": "connects a genomic feature to its sequence", "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.", + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "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.", + "in_taxon": { + "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", + "items": { + "type": "string" + }, + "type": "array" + }, + "in_taxon_label": { + "description": "The human readable scientific name for the taxon of the entity.", "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.", + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "predicate": { - "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", + "name": { + "description": "A human-readable name for an attribute or entity.", "type": "string" }, - "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.", + "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" + }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, + "type": { + "items": { + "type": "string" + }, + "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" + } + }, + "required": [ + "id", + "category" + ], + "title": "Genome", + "type": "object" + }, + "GenomeAnnotation": { + "additionalProperties": false, + "description": "Location and nomenclature of genes and all of the coding regions in a genome assembly and the classification of genes and transcripts into types.", + "properties": { + "authority": { + "description": "The organization responsible for publishing the data.", "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.", + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", + "type": "string" + }, + "type": "array" + }, + "content_url": { + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "digest": { + "description": "Stores checksum information.", "items": { "type": "string" }, "type": "array" }, - "qualifiers": { - "description": "connects an association to qualifiers that modify or qualify the meaning of that association", + "full_name": { + "description": "a long-form human readable name for a thing", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", "items": { "type": "string" }, "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.", + "has_biological_sequence": { + "description": "connects a genomic feature to its sequence", + "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" + }, + "in_taxon": { + "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": { "type": "string" }, "type": "array" }, - "subject": { - "description": "gene, product or macromolecular complex that has the function associated with the GO term", + "in_taxon_label": { + "description": "The human readable scientific name for the taxon of the entity.", "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.", + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", "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.", + "name": { + "description": "A human-readable name for an attribute or entity.", + "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" }, - "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.", + "reference_assembly": { + "type": "string" + }, + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, "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.", + "type": { "items": { "type": "string" }, "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" - }, - "timepoint": { - "description": "a point in time", - "format": "time", + "version": { "type": "string" }, - "type": { - "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", + "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" }, @@ -14416,28 +16670,21 @@ } }, "required": [ - "subject", - "predicate", - "object", - "id" + "digest", + "id", + "category" ], - "title": "GeneToGoTermAssociation", + "title": "GenomeAnnotation", "type": "object" }, - "GeneToPathwayAssociation": { + "GenomeAssembly": { "additionalProperties": false, - "description": "An interaction between a gene or gene product and a biological process or pathway.", + "description": "Genome assembly to contain version and label information", "properties": { - "aggregator_knowledge_source": { - "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", - "items": { - "type": "string" - }, - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" @@ -14446,6 +16693,10 @@ "description": "a human-readable description of an entity", "type": "string" }, + "full_name": { + "description": "a long-form human readable name for a thing", + "type": "string" + }, "has_attribute": { "description": "connects any entity to an attribute", "items": { @@ -14453,147 +16704,174 @@ }, "type": "array" }, - "has_evidence": { - "description": "connects an association to an instance of supporting evidence", + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "in_taxon": { + "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": { "type": "string" }, "type": "array" }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "in_taxon_label": { + "description": "The human readable scientific name for the taxon of the entity.", "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "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" - }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" }, - "negated": { - "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" - }, - "object": { - "description": "the pathway that includes or is affected by the gene or gene product", - "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" }, - "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.", + "strain": { + "description": "The genetic variant or subtype of a species or organism.", "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.", + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, "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.", + "type": { "items": { "type": "string" }, "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.", + "version": { + "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" + } + }, + "required": [ + "id", + "category" + ], + "title": "GenomeAssembly", + "type": "object" + }, + "GenomicBackgroundExposure": { + "additionalProperties": false, + "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.", + "properties": { + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", + "type": "string" + }, + "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" - }, - "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.", + "description": { + "description": "a human-readable description of an entity", "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.", + "full_name": { + "description": "a long-form human readable name for a thing", "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" + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" }, - "predicate": { - "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", + "has_attribute_type": { + "description": "connects an attribute to a class that describes it", "type": "string" }, - "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.", + "has_biological_sequence": { + "description": "connects a genomic feature to its sequence", "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.", + "has_gene_or_gene_product": { + "description": "connects an entity with one or more gene or gene products", "items": { "type": "string" }, "type": "array" }, - "qualifiers": { - "description": "connects an association to qualifiers that modify or qualify the meaning of that association", + "has_qualitative_value": { + "description": "connects an attribute to a value", + "type": "string" + }, + "has_quantitative_value": { + "description": "connects an attribute to a value", "items": { - "type": "string" + "$ref": "#/$defs/QuantityValue" }, "type": "array" }, - "retrieval_source_ids": { - "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "in_taxon": { + "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": { "type": "string" }, "type": "array" }, - "subject": { - "$ref": "#/$defs/GeneOrGeneProduct", - "description": "the gene or gene product entity that participates or influences the pathway" + "in_taxon_label": { + "description": "The human readable scientific name for the taxon of the entity.", + "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.", + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", "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" + "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" }, - "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.", + "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" }, - "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.", + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, "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" - }, "timepoint": { "description": "a point in time", "format": "time", "type": "string" }, "type": { - "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", + "items": { + "type": "string" + }, + "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" }, @@ -14601,17 +16879,16 @@ } }, "required": [ - "subject", - "predicate", - "object", - "id" + "id", + "has_attribute_type", + "category" ], - "title": "GeneToPathwayAssociation", + "title": "GenomicBackgroundExposure", "type": "object" }, - "GeneToPhenotypicFeatureAssociation": { + "GenomicSequenceLocalization": { "additionalProperties": false, - "description": "", + "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.", "properties": { "aggregator_knowledge_source": { "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", @@ -14631,9 +16908,13 @@ "description": "a human-readable description of an entity", "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" + "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" + }, + "genome_build": { + "$ref": "#/$defs/StrandEnum", + "description": "The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens." }, "has_attribute": { "description": "connects any entity to an attribute", @@ -14642,10 +16923,6 @@ }, "type": "array" }, - "has_count": { - "description": "number of things with a particular property", - "type": "integer" - }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { @@ -14653,17 +16930,6 @@ }, "type": "array" }, - "has_percentage": { - "description": "equivalent to has quotient multiplied by 100", - "type": "number" - }, - "has_quotient": { - "type": "number" - }, - "has_total": { - "description": "total number of things in a particular reference set", - "type": "integer" - }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" @@ -14706,9 +16972,6 @@ }, "type": "array" }, - "object_direction_qualifier": { - "$ref": "#/$defs/DirectionQualifierEnum" - }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { @@ -14720,10 +16983,6 @@ "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "type": "string" }, - "onset_qualifier": { - "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", - "type": "string" - }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string" @@ -14736,6 +16995,10 @@ "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", "type": "string" }, + "phase": { + "$ref": "#/$defs/PhaseEnum", + "description": "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2." + }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string" @@ -14765,20 +17028,17 @@ }, "type": "array" }, - "severity_qualifier": { - "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", - "type": "string" + "start_interbase_coordinate": { + "description": "The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0).", + "type": "integer" }, - "sex_qualifier": { - "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "strand": { + "$ref": "#/$defs/StrandEnum", + "description": "The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand)." }, "subject": { - "$ref": "#/$defs/GeneOrGeneProduct", - "description": "gene in which variation is correlated with the phenotypic feature" - }, - "subject_aspect_qualifier": { - "$ref": "#/$defs/GeneOrGeneProductOrChemicalEntityAspectEnum" + "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.", + "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.", @@ -14828,12 +17088,12 @@ "object", "id" ], - "title": "GeneToPhenotypicFeatureAssociation", + "title": "GenomicSequenceLocalization", "type": "object" }, - "GeneticInheritance": { + "Genotype": { "additionalProperties": false, - "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.", + "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", "properties": { "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -14858,6 +17118,13 @@ }, "type": "array" }, + "has_biological_sequence": { + "description": "connects a genomic feature to its sequence", + "type": "string" + }, + "has_zygosity": { + "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" @@ -14888,83 +17155,8 @@ }, "type": "array" }, - "type": { - "items": { - "type": "string" - }, - "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" - } - }, - "required": [ - "id", - "category" - ], - "title": "GeneticInheritance", - "type": "object" - }, - "Genome": { - "additionalProperties": false, - "description": "A genome is the sum of genetic material within a cell or virion.", - "properties": { - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", - "items": { - "pattern": "^biolink:[A-Z][A-Za-z]+$", - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a human-readable description of an entity", - "type": "string" - }, - "full_name": { - "description": "a long-form human readable name for a thing", - "type": "string" - }, - "has_attribute": { - "description": "connects any entity to an attribute", - "items": { - "type": "string" - }, - "type": "array" - }, - "has_biological_sequence": { - "description": "connects a genomic feature to its sequence", - "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" - }, - "in_taxon": { - "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", - "items": { - "type": "string" - }, - "type": "array" - }, - "in_taxon_label": { - "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" - }, - "iri": { - "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" - }, - "name": { - "description": "A human-readable name for an attribute or entity.", - "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.", + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, @@ -14988,22 +17180,22 @@ "id", "category" ], - "title": "Genome", + "title": "Genotype", "type": "object" }, - "GenomeAnnotation": { + "GenotypeAsAModelOfDiseaseAssociation": { "additionalProperties": false, - "description": "Location and nomenclature of genes and all of the coding regions in a genome assembly and the classification of genes and transcripts into types.", + "description": "", "properties": { - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "aggregator_knowledge_source": { + "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", "items": { - "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" }, - "content_url": { + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { "type": "string" }, @@ -15013,14 +17205,8 @@ "description": "a human-readable description of an entity", "type": "string" }, - "digest": { - "items": { - "type": "string" - }, - "type": "array" - }, - "full_name": { - "description": "a long-form human readable name for a thing", + "frequency_qualifier": { + "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", "type": "string" }, "has_attribute": { @@ -15030,187 +17216,155 @@ }, "type": "array" }, - "has_biological_sequence": { - "description": "connects a genomic feature to its sequence", - "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" - }, - "in_taxon": { - "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", + "has_evidence": { + "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, "type": "array" }, - "in_taxon_label": { - "description": "The human readable scientific name for the taxon of the entity.", + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, + "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" + }, "name": { "description": "A human-readable name for an attribute or entity.", "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" + "negated": { + "description": "if set to true, then the association is negated i.e. is not true", + "type": "boolean" }, - "reference_assembly": { + "object": { + "description": "disease", "type": "string" }, - "type": { - "items": { - "type": "string" - }, - "type": "array" - }, - "version": { + "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" }, - "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.", + "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" - } - }, - "required": [ - "digest", - "id", - "category" - ], - "title": "GenomeAnnotation", - "type": "object" - }, - "GenomeAssembly": { - "additionalProperties": false, - "description": "Genome assembly to contain version and label information", - "properties": { - "description": { - "type": "string" - }, - "id": { - "type": "string" - }, - "label": { - "type": "string" - }, - "taxon": { - "type": "string" }, - "version": { - "type": "string" - } - }, - "title": "GenomeAssembly", - "type": "object" - }, - "GenomicBackgroundExposure": { - "additionalProperties": false, - "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.", - "properties": { - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "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": { - "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" }, - "description": { - "description": "a human-readable description of an entity", - "type": "string" - }, - "full_name": { - "description": "a long-form human readable name for a thing", - "type": "string" - }, - "has_attribute": { - "description": "connects any entity to an attribute", + "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" }, - "has_attribute_type": { - "description": "connects an attribute to a class that describes it", + "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" }, - "has_biological_sequence": { - "description": "connects a genomic feature to its sequence", + "onset_qualifier": { + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", "type": "string" }, - "has_gene_or_gene_product": { - "description": "connects an entity with one or more gene or gene products", + "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" + }, + "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" + }, + "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" + }, + "predicate": { + "description": "The relationship to the disease", + "type": "string" + }, + "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" + }, + "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" }, - "has_qualitative_value": { - "description": "connects an attribute to a value", - "type": "string" - }, - "has_quantitative_value": { - "description": "connects an attribute to a value", + "qualifiers": { + "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { - "$ref": "#/$defs/QuantityValue" + "type": "string" }, "type": "array" }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", - "type": "string" - }, - "in_taxon": { - "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", + "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" }, - "in_taxon_label": { - "description": "The human readable scientific name for the taxon of the entity.", + "severity_qualifier": { + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string" }, - "iri": { - "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "subject": { + "description": "A genotype that has a role in modeling the disease.", "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.", + "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" }, - "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.", + "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" }, - "timepoint": { - "description": "a point in time", - "format": "time", - "type": "string" + "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" }, - "type": { + "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" }, - "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.", + "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" + }, + "timepoint": { + "description": "a point in time", + "format": "time", + "type": "string" + }, + "type": { + "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, @@ -15218,16 +17372,17 @@ } }, "required": [ - "id", - "has_attribute_type", - "category" + "subject", + "predicate", + "object", + "id" ], - "title": "GenomicBackgroundExposure", + "title": "GenotypeAsAModelOfDiseaseAssociation", "type": "object" }, - "GenomicSequenceLocalization": { + "GenotypeToDiseaseAssociation": { "additionalProperties": false, - "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.", + "description": "", "properties": { "aggregator_knowledge_source": { "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", @@ -15247,13 +17402,9 @@ "description": "a human-readable description of an entity", "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" - }, - "genome_build": { - "$ref": "#/$defs/StrandEnum", - "description": "The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens." + "frequency_qualifier": { + "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", + "type": "string" }, "has_attribute": { "description": "connects any entity to an attribute", @@ -15290,7 +17441,7 @@ "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.", + "description": "a disease that is associated with that genotype", "type": "string" }, "object_category": { @@ -15322,6 +17473,10 @@ "description": "Used to 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" }, + "onset_qualifier": { + "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "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" @@ -15334,12 +17489,8 @@ "description": "used 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" }, - "phase": { - "$ref": "#/$defs/PhaseEnum", - "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." - }, "predicate": { - "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", + "description": "E.g. is pathogenic for", "type": "string" }, "primary_knowledge_source": { @@ -15367,16 +17518,12 @@ }, "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" - }, - "strand": { - "$ref": "#/$defs/StrandEnum", - "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)." + "severity_qualifier": { + "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", + "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.", + "description": "a genotype that is associated in some way with a disease state", "type": "string" }, "subject_category": { @@ -15427,17 +17574,23 @@ "object", "id" ], - "title": "GenomicSequenceLocalization", + "title": "GenotypeToDiseaseAssociation", "type": "object" }, - "Genotype": { + "GenotypeToGeneAssociation": { "additionalProperties": false, - "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", + "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", "properties": { + "aggregator_knowledge_source": { + "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", + "items": { + "type": "string" + }, + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { - "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" @@ -15446,10 +17599,6 @@ "description": "a human-readable description of an entity", "type": "string" }, - "full_name": { - "description": "a long-form human readable name for a thing", - "type": "string" - }, "has_attribute": { "description": "connects any entity to an attribute", "items": { @@ -15457,51 +17606,147 @@ }, "type": "array" }, - "has_biological_sequence": { - "description": "connects a genomic feature to its sequence", + "has_evidence": { + "description": "connects an association to an instance of supporting evidence", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, - "has_zygosity": { + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "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" }, - "in_taxon": { - "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", + "name": { + "description": "A human-readable name for an attribute or entity.", + "type": "string" + }, + "negated": { + "description": "if set to true, then the association is negated i.e. is not true", + "type": "boolean" + }, + "object": { + "description": "gene implicated in genotype", + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "predicate": { + "description": "the relationship type used to connect genotype to gene", + "type": "string" + }, + "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" + }, + "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" + }, + "qualifiers": { + "description": "connects an association to qualifiers that modify or qualify the meaning of that association", + "items": { + "type": "string" + }, + "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" }, - "in_taxon_label": { - "description": "The human readable scientific name for the taxon of the entity.", + "subject": { + "description": "parent genotype", "type": "string" }, - "iri": { - "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "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" }, - "name": { - "description": "A human-readable name for an attribute or entity.", - "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" }, - "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.", + "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" }, - "type": { + "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" }, - "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.", + "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" + }, + "timepoint": { + "description": "a point in time", + "format": "time", + "type": "string" + }, + "type": { + "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, @@ -15509,15 +17754,17 @@ } }, "required": [ - "id", - "category" + "subject", + "predicate", + "object", + "id" ], - "title": "Genotype", + "title": "GenotypeToGeneAssociation", "type": "object" }, - "GenotypeAsAModelOfDiseaseAssociation": { + "GenotypeToGenotypePartAssociation": { "additionalProperties": false, - "description": "", + "description": "Any association between one genotype and a genotypic entity that is a sub-component of it", "properties": { "aggregator_knowledge_source": { "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", @@ -15537,10 +17784,6 @@ "description": "a human-readable description of an entity", "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" - }, "has_attribute": { "description": "connects any entity to an attribute", "items": { @@ -15576,7 +17819,7 @@ "type": "boolean" }, "object": { - "description": "disease", + "description": "child genotype", "type": "string" }, "object_category": { @@ -15608,10 +17851,6 @@ "description": "Used to 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" }, - "onset_qualifier": { - "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", - "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" @@ -15625,7 +17864,7 @@ "type": "string" }, "predicate": { - "description": "The relationship to the disease", + "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string" }, "primary_knowledge_source": { @@ -15653,12 +17892,8 @@ }, "type": "array" }, - "severity_qualifier": { - "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", - "type": "string" - }, "subject": { - "description": "A genotype that has a role in modeling the disease.", + "description": "parent genotype", "type": "string" }, "subject_category": { @@ -15709,12 +17944,12 @@ "object", "id" ], - "title": "GenotypeAsAModelOfDiseaseAssociation", + "title": "GenotypeToGenotypePartAssociation", "type": "object" }, - "GenotypeToDiseaseAssociation": { + "GenotypeToPhenotypicFeatureAssociation": { "additionalProperties": false, - "description": "", + "description": "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment", "properties": { "aggregator_knowledge_source": { "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", @@ -15745,6 +17980,10 @@ }, "type": "array" }, + "has_count": { + "description": "number of things with a particular property", + "type": "integer" + }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { @@ -15752,6 +17991,17 @@ }, "type": "array" }, + "has_percentage": { + "description": "equivalent to has quotient multiplied by 100", + "type": "number" + }, + "has_quotient": { + "type": "number" + }, + "has_total": { + "description": "total number of things in a particular reference set", + "type": "integer" + }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" @@ -15773,7 +18023,7 @@ "type": "boolean" }, "object": { - "description": "a disease that is associated with that genotype", + "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", "type": "string" }, "object_category": { @@ -15822,7 +18072,7 @@ "type": "string" }, "predicate": { - "description": "E.g. is pathogenic for", + "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", "type": "string" }, "primary_knowledge_source": { @@ -15854,8 +18104,12 @@ "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", "type": "string" }, + "sex_qualifier": { + "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", + "type": "string" + }, "subject": { - "description": "a genotype that is associated in some way with a disease state", + "description": "genotype that is associated with the phenotypic feature", "type": "string" }, "subject_category": { @@ -15906,12 +18160,12 @@ "object", "id" ], - "title": "GenotypeToDiseaseAssociation", + "title": "GenotypeToPhenotypicFeatureAssociation", "type": "object" }, - "GenotypeToGeneAssociation": { + "GenotypeToVariantAssociation": { "additionalProperties": false, - "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", + "description": "Any association between a genotype and a sequence variant.", "properties": { "aggregator_knowledge_source": { "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", @@ -16091,23 +18345,17 @@ "object", "id" ], - "title": "GenotypeToGeneAssociation", + "title": "GenotypeToVariantAssociation", "type": "object" }, - "GenotypeToGenotypePartAssociation": { + "GenotypicSex": { "additionalProperties": false, - "description": "Any association between one genotype and a genotypic entity that is a sub-component of it", + "description": "An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes.", "properties": { - "aggregator_knowledge_source": { - "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", - "items": { - "type": "string" - }, - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" @@ -16116,6 +18364,10 @@ "description": "a human-readable description of an entity", "type": "string" }, + "full_name": { + "description": "a long-form human readable name for a thing", + "type": "string" + }, "has_attribute": { "description": "connects any entity to an attribute", "items": { @@ -16123,10 +18375,18 @@ }, "type": "array" }, - "has_evidence": { - "description": "connects an association to an instance of supporting evidence", + "has_attribute_type": { + "description": "connects an attribute to a class that describes it", + "type": "string" + }, + "has_qualitative_value": { + "description": "connects an attribute to a value", + "type": "string" + }, + "has_quantitative_value": { + "description": "connects an attribute to a value", "items": { - "type": "string" + "$ref": "#/$defs/QuantityValue" }, "type": "array" }, @@ -16138,132 +18398,127 @@ "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "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" - }, "name": { - "description": "A human-readable name for an attribute or entity.", - "type": "string" - }, - "negated": { - "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" - }, - "object": { - "description": "child genotype", - "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.", + "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" }, - "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.", + "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" }, - "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.", + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, "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.", + "type": { "items": { "type": "string" }, "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" - }, - "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" - }, - "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" - }, - "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" - }, - "predicate": { - "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", - "type": "string" - }, - "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" - }, - "publications": { - "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", + "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" - }, - "qualifiers": { - "description": "connects an association to qualifiers that modify or qualify the meaning of that association", + } + }, + "required": [ + "has_attribute_type", + "id", + "category" + ], + "title": "GenotypicSex", + "type": "object" + }, + "GeographicExposure": { + "additionalProperties": false, + "description": "A geographic exposure is a factor relating to geographic proximity to some impactful entity.", + "properties": { + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" }, - "retrieval_source_ids": { - "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "full_name": { + "description": "a long-form human readable name for a thing", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", "items": { "type": "string" }, "type": "array" }, - "subject": { - "description": "parent genotype", + "has_attribute_type": { + "description": "connects an attribute to a class that describes it", "type": "string" }, - "subject_category": { - "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", + "has_qualitative_value": { + "description": "connects an attribute to a value", "type": "string" }, - "subject_category_closure": { - "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", + "has_quantitative_value": { + "description": "connects an attribute to a value", "items": { - "type": "string" + "$ref": "#/$defs/QuantityValue" }, "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.", + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "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" + }, + "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" }, - "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.", + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, "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" - }, "timepoint": { "description": "a point in time", "format": "time", "type": "string" }, "type": { - "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", + "items": { + "type": "string" + }, + "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" }, @@ -16271,28 +18526,21 @@ } }, "required": [ - "subject", - "predicate", - "object", - "id" + "has_attribute_type", + "id", + "category" ], - "title": "GenotypeToGenotypePartAssociation", + "title": "GeographicExposure", "type": "object" }, - "GenotypeToPhenotypicFeatureAssociation": { + "GeographicLocation": { "additionalProperties": false, - "description": "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment", + "description": "a location that can be described in lat/long coordinates", "properties": { - "aggregator_knowledge_source": { - "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", - "items": { - "type": "string" - }, - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" @@ -16301,8 +18549,8 @@ "description": "a human-readable description of an entity", "type": "string" }, - "frequency_qualifier": { - "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", + "full_name": { + "description": "a long-form human readable name for a thing", "type": "string" }, "has_attribute": { @@ -16312,28 +18560,6 @@ }, "type": "array" }, - "has_count": { - "description": "number of things with a particular property", - "type": "integer" - }, - "has_evidence": { - "description": "connects an association to an instance of supporting evidence", - "items": { - "type": "string" - }, - "type": "array" - }, - "has_percentage": { - "description": "equivalent to has quotient multiplied by 100", - "type": "number" - }, - "has_quotient": { - "type": "number" - }, - "has_total": { - "description": "total number of things in a particular reference set", - "type": "integer" - }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" @@ -16342,144 +18568,212 @@ "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "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" + "latitude": { + "description": "latitude", + "type": "number" + }, + "longitude": { + "description": "longitude", + "type": "number" }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" }, - "negated": { - "description": "if set to true, then the association is negated i.e. is not true", - "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.", - "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" + "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" }, - "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.", + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, "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.", + "type": { "items": { "type": "string" }, "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.", + "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" + } + }, + "required": [ + "id", + "category" + ], + "title": "GeographicLocation", + "type": "object" + }, + "GeographicLocationAtTime": { + "additionalProperties": false, + "description": "a location that can be described in lat/long coordinates, for a particular time", + "properties": { + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "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.", + "description": { + "description": "a human-readable description of an entity", "type": "string" }, - "onset_qualifier": { - "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject", + "full_name": { + "description": "a long-form human readable name for a thing", "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" + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" }, - "original_predicate": { - "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "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.", + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "predicate": { - "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", - "type": "string" + "latitude": { + "description": "latitude", + "type": "number" }, - "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.", + "longitude": { + "description": "longitude", + "type": "number" + }, + "name": { + "description": "A human-readable name for an attribute or entity.", "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.", + "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" }, - "qualifiers": { - "description": "connects an association to qualifiers that modify or qualify the meaning of that association", + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, "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.", + "timepoint": { + "description": "a point in time", + "format": "time", + "type": "string" + }, + "type": { "items": { "type": "string" }, "type": "array" }, - "severity_qualifier": { - "description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject", - "type": "string" - }, - "sex_qualifier": { - "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "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" + } + }, + "required": [ + "id", + "category" + ], + "title": "GeographicLocationAtTime", + "type": "object" + }, + "GrossAnatomicalStructure": { + "additionalProperties": false, + "description": "", + "properties": { + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", + "type": "string" + }, + "type": "array" }, - "subject": { - "description": "genotype that is associated with the phenotypic feature", + "description": { + "description": "a human-readable description of an entity", "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.", + "full_name": { + "description": "a long-form human readable name for a thing", "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.", + "has_attribute": { + "description": "may often be an organism attribute", "items": { "type": "string" }, "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.", + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "in_taxon": { + "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": { "type": "string" }, "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.", + "in_taxon_label": { + "description": "The human readable scientific name for the taxon of the entity.", + "type": "string" + }, + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "type": "string" + }, + "name": { + "description": "A human-readable name for an attribute or entity.", + "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" }, - "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" - }, - "timepoint": { - "description": "a point in time", - "format": "time", - "type": "string" + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" }, "type": { - "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", + "items": { + "type": "string" + }, + "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" }, @@ -16487,28 +18781,20 @@ } }, "required": [ - "subject", - "predicate", - "object", - "id" + "id", + "category" ], - "title": "GenotypeToPhenotypicFeatureAssociation", + "title": "GrossAnatomicalStructure", "type": "object" }, - "GenotypeToVariantAssociation": { + "Haplotype": { "additionalProperties": false, - "description": "Any association between a genotype and a sequence variant.", + "description": "A set of zero or more Alleles on a single instance of a Sequence[VMC]", "properties": { - "aggregator_knowledge_source": { - "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", - "items": { - "type": "string" - }, - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" @@ -16517,6 +18803,10 @@ "description": "a human-readable description of an entity", "type": "string" }, + "full_name": { + "description": "a long-form human readable name for a thing", + "type": "string" + }, "has_attribute": { "description": "connects any entity to an attribute", "items": { @@ -16524,147 +18814,129 @@ }, "type": "array" }, - "has_evidence": { - "description": "connects an association to an instance of supporting evidence", + "has_biological_sequence": { + "description": "connects a genomic feature to its sequence", + "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" + }, + "in_taxon": { + "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": { "type": "string" }, "type": "array" }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "in_taxon_label": { + "description": "The human readable scientific name for the taxon of the entity.", "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "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" - }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" }, - "negated": { - "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" - }, - "object": { - "description": "gene implicated in genotype", - "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" - }, - "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.", + "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" }, - "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.", + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, "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.", + "type": { "items": { "type": "string" }, "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" - }, - "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" - }, - "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" - }, - "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" - }, - "predicate": { - "description": "the relationship type used to connect genotype to gene", - "type": "string" - }, - "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" - }, - "publications": { - "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", + "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" - }, - "qualifiers": { - "description": "connects an association to qualifiers that modify or qualify the meaning of that association", + } + }, + "required": [ + "id", + "category" + ], + "title": "Haplotype", + "type": "object" + }, + "Hospitalization": { + "additionalProperties": false, + "description": "", + "properties": { + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "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.", + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "full_name": { + "description": "a long-form human readable name for a thing", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", "items": { "type": "string" }, "type": "array" }, - "subject": { - "description": "parent genotype", + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "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.", + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", "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.", + "name": { + "description": "A human-readable name for an attribute or entity.", + "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" }, - "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.", + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, "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.", + "type": { "items": { "type": "string" }, "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" - }, - "timepoint": { - "description": "a point in time", - "format": "time", - "type": "string" - }, - "type": { - "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", + "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" }, @@ -16672,17 +18944,21 @@ } }, "required": [ - "subject", - "predicate", - "object", - "id" + "id", + "category" ], - "title": "GenotypeToVariantAssociation", + "title": "Hospitalization", "type": "object" }, - "GenotypicSex": { + "HospitalizationOutcome": { "additionalProperties": false, - "description": "An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes.", + "description": "An outcome resulting from an exposure event which is the increased manifestation of acute (e.g. emergency room visit) or chronic (inpatient) hospitalization.", + "title": "HospitalizationOutcome", + "type": "object" + }, + "Human": { + "additionalProperties": false, + "description": "A member of the the species Homo sapiens.", "properties": { "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -16701,29 +18977,25 @@ "type": "string" }, "has_attribute": { - "description": "connects any entity to an attribute", + "description": "may often be an organism attribute", "items": { "type": "string" }, "type": "array" }, - "has_attribute_type": { - "description": "connects an attribute to a class that describes it", - "type": "string" - }, - "has_qualitative_value": { - "description": "connects an attribute to a value", + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, - "has_quantitative_value": { - "description": "connects an attribute to a value", + "in_taxon": { + "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": { - "$ref": "#/$defs/QuantityValue" + "type": "string" }, "type": "array" }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "in_taxon_label": { + "description": "The human readable scientific name for the taxon of the entity.", "type": "string" }, "iri": { @@ -16731,7 +19003,7 @@ "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.", + "description": "A human-readable name for an attribute or entity.", "type": "string" }, "provided_by": { @@ -16741,6 +19013,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -16756,16 +19035,15 @@ } }, "required": [ - "has_attribute_type", "id", "category" ], - "title": "GenotypicSex", + "title": "Human", "type": "object" }, - "GeographicExposure": { + "IndividualOrganism": { "additionalProperties": false, - "description": "A geographic exposure is a factor relating to geographic proximity to some impactful entity.", + "description": "An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576", "properties": { "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -16784,29 +19062,25 @@ "type": "string" }, "has_attribute": { - "description": "connects any entity to an attribute", + "description": "may often be an organism attribute", "items": { "type": "string" }, "type": "array" }, - "has_attribute_type": { - "description": "connects an attribute to a class that describes it", - "type": "string" - }, - "has_qualitative_value": { - "description": "connects an attribute to a value", + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, - "has_quantitative_value": { - "description": "connects an attribute to a value", + "in_taxon": { + "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", "items": { - "$ref": "#/$defs/QuantityValue" + "type": "string" }, "type": "array" }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "in_taxon_label": { + "description": "The human readable scientific name for the taxon of the entity.", "type": "string" }, "iri": { @@ -16814,7 +19088,7 @@ "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.", + "description": "A human-readable name for an attribute or entity.", "type": "string" }, "provided_by": { @@ -16824,11 +19098,13 @@ }, "type": "array" }, - "timepoint": { - "description": "a point in time", - "format": "time", - "type": "string" - }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -16844,21 +19120,26 @@ } }, "required": [ - "has_attribute_type", "id", "category" ], - "title": "GeographicExposure", + "title": "IndividualOrganism", "type": "object" }, - "GeographicLocation": { + "InformationContentEntityToNamedThingAssociation": { "additionalProperties": false, - "description": "a location that can be described in lat/long coordinates", + "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).", "properties": { + "aggregator_knowledge_source": { + "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", + "items": { + "type": "string" + }, + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { - "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" @@ -16867,10 +19148,6 @@ "description": "a human-readable description of an entity", "type": "string" }, - "full_name": { - "description": "a long-form human readable name for a thing", - "type": "string" - }, "has_attribute": { "description": "connects any entity to an attribute", "items": { @@ -16878,6 +19155,13 @@ }, "type": "array" }, + "has_evidence": { + "description": "connects an association to an instance of supporting evidence", + "items": { + "type": "string" + }, + "type": "array" + }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" @@ -16886,113 +19170,132 @@ "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "latitude": { - "description": "latitude", - "type": "number" - }, - "longitude": { - "description": "longitude", - "type": "number" + "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" }, "name": { "description": "A human-readable name for an attribute or entity.", "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.", + "negated": { + "description": "if set to true, then the association is negated i.e. is not true", + "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.", + "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" + }, + "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" }, - "type": { + "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" }, - "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.", + "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" - } - }, - "required": [ - "id", - "category" - ], - "title": "GeographicLocation", - "type": "object" - }, - "GeographicLocationAtTime": { - "additionalProperties": false, - "description": "a location that can be described in lat/long coordinates, for a particular time", - "properties": { - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + }, + "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" + }, + "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" + }, + "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" + }, + "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" + }, + "predicate": { + "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", + "type": "string" + }, + "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" + }, + "publications": { + "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { - "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" }, - "description": { - "description": "a human-readable description of an entity", - "type": "string" - }, - "full_name": { - "description": "a long-form human readable name for a thing", - "type": "string" + "qualifiers": { + "description": "connects an association to qualifiers that modify or qualify the meaning of that association", + "items": { + "type": "string" + }, + "type": "array" }, - "has_attribute": { - "description": "connects any entity to an attribute", + "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" }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "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.", "type": "string" }, - "iri": { - "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "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" }, - "latitude": { - "description": "latitude", - "type": "number" - }, - "longitude": { - "description": "longitude", - "type": "number" + "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" }, - "name": { - "description": "A human-readable name for an attribute or entity.", - "type": "string" + "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" }, - "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.", + "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" }, + "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" + }, "timepoint": { "description": "a point in time", "format": "time", "type": "string" }, "type": { - "items": { - "type": "string" - }, - "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.", + "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, @@ -17000,15 +19303,17 @@ } }, "required": [ - "id", - "category" + "subject", + "predicate", + "object", + "id" ], - "title": "GeographicLocationAtTime", + "title": "InformationContentEntityToNamedThingAssociation", "type": "object" }, - "GrossAnatomicalStructure": { + "Invertebrate": { "additionalProperties": false, - "description": "", + "description": "An animal lacking a vertebral column. This group consists of 98% of all animal species.", "properties": { "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -17063,6 +19368,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -17081,13 +19393,20 @@ "id", "category" ], - "title": "GrossAnatomicalStructure", + "title": "Invertebrate", "type": "object" }, - "Haplotype": { + "JournalArticle": { "additionalProperties": false, - "description": "A set of zero or more Alleles on a single instance of a Sequence[VMC]", + "description": "an article, typically presenting results of research, that is published in an issue of a scientific journal.", "properties": { + "authors": { + "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.", + "items": { + "type": "string" + }, + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { @@ -17096,10 +19415,18 @@ }, "type": "array" }, + "creation_date": { + "description": "date on which an entity was created. This can be applied to nodes or edges", + "format": "date", + "type": "string" + }, "description": { "description": "a human-readable description of an entity", "type": "string" }, + "format": { + "type": "string" + }, "full_name": { "description": "a long-form human readable name for a thing", "type": "string" @@ -17111,35 +19438,70 @@ }, "type": "array" }, - "has_biological_sequence": { - "description": "connects a genomic feature to its sequence", + "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.", "type": "string" }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, - "in_taxon": { - "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", + "iso_abbreviation": { + "description": "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent.", + "type": "string" + }, + "issue": { + "description": "issue of a newspaper, a scientific journal or magazine for reference purpose", + "type": "string" + }, + "keywords": { + "description": "keywords tagging a publication", + "items": { + "type": "string" + }, + "type": "array" + }, + "license": { + "type": "string" + }, + "mesh_terms": { + "description": "mesh terms tagging a publication", + "items": { + "type": "string" + }, + "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" + }, + "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" + }, + "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" }, - "in_taxon_label": { - "description": "The human readable scientific name for the taxon of the entity.", + "published_in": { + "description": "The enclosing parent serial containing the article should have industry-standard identifier from ISSN.", "type": "string" }, - "iri": { - "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "rights": { "type": "string" }, - "name": { - "description": "A human-readable name for an attribute or entity.", + "summary": { + "description": "executive summary of a publication", "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.", + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, @@ -17151,6 +19513,10 @@ }, "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" + }, "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": { @@ -17160,30 +19526,35 @@ } }, "required": [ + "published_in", "id", "category" ], - "title": "Haplotype", + "title": "JournalArticle", "type": "object" }, - "Hospitalization": { + "Library": { "additionalProperties": false, "description": "", "properties": { + "avg_size_bp": { + "description": "The average size (bp) of the library fragments.", + "type": "integer" + }, "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { - "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" }, - "description": { - "description": "a human-readable description of an entity", + "creation_date": { + "description": "The date and time the object was created.", + "format": "date-time", "type": "string" }, - "full_name": { - "description": "a long-form human readable name for a thing", + "description": { + "description": "a human-readable description of an entity", "type": "string" }, "has_attribute": { @@ -17197,56 +19568,84 @@ "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, + "input_quantity": { + "description": "The amount of input material (ng) used to create the library.", + "type": "number" + }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" }, + "method": { + "type": "string" + }, "name": { "description": "A human-readable name for an attribute or entity.", "type": "string" }, - "provided_by": { - "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", + "process_pass": { + "description": "Indicates whether the library prep process passed or failed.", + "type": "boolean" + }, + "quantification_fmol": { + "type": "number" + }, + "quantification_ng": { + "type": "number" + }, + "quantification_nm": { + "type": "number" + }, + "r1_index": { + "type": "string" + }, + "r1_sequence": { + "type": "string" + }, + "r2_index": { + "type": "string" + }, + "r2_sequence": { + "type": "string" + }, + "type": { "items": { "type": "string" }, "type": "array" }, - "type": { + "wasAttributedTo": { "items": { - "type": "string" + "$ref": "#/$defs/Agent" }, "type": "array" }, - "xref": { - "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", + "wasDerivedFrom": { "items": { - "type": "string" + "$ref": "#/$defs/AmplifiedCdna" + }, + "type": "array" + }, + "wasGeneratedBy": { + "items": { + "$ref": "#/$defs/LibraryConstruction" }, "type": "array" } }, "required": [ - "id", - "category" + "id" ], - "title": "Hospitalization", - "type": "object" - }, - "HospitalizationOutcome": { - "additionalProperties": false, - "description": "An outcome resulting from an exposure event which is the increased manifestation of acute (e.g. emergency room visit) or chronic (inpatient) hospitalization.", - "title": "HospitalizationOutcome", + "title": "Library", "type": "object" }, - "Human": { + "LibraryAliquot": { "additionalProperties": false, - "description": "A member of the the species Homo sapiens.", + "description": "", "properties": { "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { - "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" @@ -17255,12 +19654,8 @@ "description": "a human-readable description of an entity", "type": "string" }, - "full_name": { - "description": "a long-form human readable name for a thing", - "type": "string" - }, "has_attribute": { - "description": "may often be an organism attribute", + "description": "connects any entity to an attribute", "items": { "type": "string" }, @@ -17270,16 +19665,9 @@ "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, - "in_taxon": { - "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", - "items": { - "type": "string" - }, - "type": "array" - }, - "in_taxon_label": { - "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "input_quantity": { + "description": "The amount of input material (fmol) used to create the library aliquot.", + "type": "integer" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", @@ -17289,37 +19677,40 @@ "description": "A human-readable name for an attribute or entity.", "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.", + "type": { "items": { "type": "string" }, "type": "array" }, - "type": { + "wasAttributedTo": { "items": { - "type": "string" + "$ref": "#/$defs/Agent" }, "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.", + "wasDerivedFrom": { "items": { - "type": "string" + "$ref": "#/$defs/Library" + }, + "type": "array" + }, + "wasGeneratedBy": { + "items": { + "$ref": "#/$defs/LibraryAliquoting" }, "type": "array" } }, "required": [ - "id", - "category" + "id" ], - "title": "Human", + "title": "LibraryAliquot", "type": "object" }, - "IndividualOrganism": { + "LibraryAliquoting": { "additionalProperties": false, - "description": "An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576", + "description": "A process that takes a library and produces an library aliquot.", "properties": { "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -17337,26 +19728,21 @@ "description": "a long-form human readable name for a thing", "type": "string" }, - "has_attribute": { - "description": "may often be an organism attribute", + "generated": { "items": { - "type": "string" + "$ref": "#/$defs/LibraryAliquot" }, "type": "array" }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", - "type": "string" - }, - "in_taxon": { - "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", + "has_attribute": { + "description": "connects any entity to an attribute", "items": { "type": "string" }, "type": "array" }, - "in_taxon_label": { - "description": "The human readable scientific name for the taxon of the entity.", + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, "iri": { @@ -17374,12 +19760,31 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" }, "type": "array" }, + "used": { + "items": { + "$ref": "#/$defs/Library" + }, + "type": "array" + }, + "wasAssociatedWith": { + "items": { + "$ref": "#/$defs/Agent" + }, + "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": { @@ -17392,23 +19797,17 @@ "id", "category" ], - "title": "IndividualOrganism", + "title": "LibraryAliquoting", "type": "object" }, - "InformationContentEntityToNamedThingAssociation": { + "LibraryConstruction": { "additionalProperties": false, - "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).", + "description": "A process that takes an amplified cDNA sample and produces a library.", "properties": { - "aggregator_knowledge_source": { - "description": "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.", - "items": { - "type": "string" - }, - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" @@ -17417,154 +19816,69 @@ "description": "a human-readable description of an entity", "type": "string" }, - "has_attribute": { - "description": "connects any entity to an attribute", - "items": { - "type": "string" - }, - "type": "array" - }, - "has_evidence": { - "description": "connects an association to an instance of supporting evidence", - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", - "type": "string" - }, - "iri": { - "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" - }, - "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" - }, - "name": { - "description": "A human-readable name for an attribute or entity.", - "type": "string" - }, - "negated": { - "description": "if set to true, then the association is negated i.e. is not true", - "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.", - "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" - }, - "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" - }, - "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" - }, - "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" - }, - "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" - }, - "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" - }, - "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" - }, - "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" - }, - "predicate": { - "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", - "type": "string" - }, - "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.", + "full_name": { + "description": "a long-form human readable name for a thing", "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" - }, - "qualifiers": { - "description": "connects an association to qualifiers that modify or qualify the meaning of that association", + }, + "generated": { "items": { - "type": "string" + "$ref": "#/$defs/Library" }, "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.", + "has_attribute": { + "description": "connects any entity to an attribute", "items": { "type": "string" }, "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.", + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "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.", + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", "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.", + "name": { + "description": "A human-readable name for an attribute or entity.", + "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" }, - "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.", + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, "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.", + "type": { "items": { "type": "string" }, "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" + "used": { + "items": { + "$ref": "#/$defs/AmplifiedCdna" + }, + "type": "array" }, - "timepoint": { - "description": "a point in time", - "format": "time", - "type": "string" + "wasAssociatedWith": { + "items": { + "$ref": "#/$defs/Agent" + }, + "type": "array" }, - "type": { - "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", + "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" }, @@ -17572,22 +19886,23 @@ } }, "required": [ - "subject", - "predicate", - "object", - "id" + "id", + "category" ], - "title": "InformationContentEntityToNamedThingAssociation", + "title": "LibraryConstruction", "type": "object" }, - "Invertebrate": { + "LibraryPool": { "additionalProperties": false, - "description": "An animal lacking a vertebral column. This group consists of 98% of all animal species.", + "description": "", "properties": { + "avg_size_bp": { + "description": "The average size (bp) of the library fragments in the tube.", + "type": "integer" + }, "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { - "pattern": "^biolink:[A-Z][A-Za-z]+$", "type": "string" }, "type": "array" @@ -17596,12 +19911,8 @@ "description": "a human-readable description of an entity", "type": "string" }, - "full_name": { - "description": "a long-form human readable name for a thing", - "type": "string" - }, "has_attribute": { - "description": "may often be an organism attribute", + "description": "connects any entity to an attribute", "items": { "type": "string" }, @@ -17611,17 +19922,6 @@ "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, - "in_taxon": { - "description": "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'", - "items": { - "type": "string" - }, - "type": "array" - }, - "in_taxon_label": { - "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" - }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "type": "string" @@ -17630,45 +19930,45 @@ "description": "A human-readable name for an attribute or entity.", "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.", + "tube_contents": { + "description": "The content concentration (nm).", + "type": "number" + }, + "type": { "items": { "type": "string" }, "type": "array" }, - "type": { + "wasAttributedTo": { "items": { - "type": "string" + "$ref": "#/$defs/Agent" }, "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.", + "wasDerivedFrom": { "items": { - "type": "string" + "$ref": "#/$defs/LibraryAliquot" + }, + "type": "array" + }, + "wasGeneratedBy": { + "items": { + "$ref": "#/$defs/LibraryPooling" }, "type": "array" } }, "required": [ - "id", - "category" + "id" ], - "title": "Invertebrate", + "title": "LibraryPool", "type": "object" }, - "JournalArticle": { + "LibraryPooling": { "additionalProperties": false, - "description": "an article, typically presenting results of research, that is published in an issue of a scientific journal.", + "description": "A process that takes a library aliquot and produces a library pool.", "properties": { - "authors": { - "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.", - "items": { - "type": "string" - }, - "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", "items": { @@ -17677,22 +19977,20 @@ }, "type": "array" }, - "creation_date": { - "description": "date on which an entity was created. This can be applied to nodes or edges", - "format": "date", - "type": "string" - }, "description": { "description": "a human-readable description of an entity", "type": "string" }, - "format": { - "type": "string" - }, "full_name": { "description": "a long-form human readable name for a thing", "type": "string" }, + "generated": { + "items": { + "$ref": "#/$defs/LibraryPool" + }, + "type": "array" + }, "has_attribute": { "description": "connects any entity to an attribute", "items": { @@ -17701,77 +19999,49 @@ "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.", + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", "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" - }, - "issue": { - "description": "issue of a newspaper, a scientific journal or magazine for reference purpose", + "name": { + "description": "A human-readable name for an attribute or entity.", "type": "string" }, - "keywords": { - "description": "keywords tagging a publication", + "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" }, - "license": { - "type": "string" - }, - "mesh_terms": { - "description": "mesh terms tagging a publication", + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, "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" - }, - "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.", + "type": { "items": { "type": "string" }, "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.", + "used": { "items": { - "type": "string" + "$ref": "#/$defs/LibraryAliquot" }, "type": "array" }, - "published_in": { - "description": "The enclosing parent serial containing the article should have industry-standard identifier from ISSN.", - "type": "string" - }, - "rights": { - "type": "string" - }, - "summary": { - "description": "executive summary of a publication", - "type": "string" - }, - "type": { + "wasAssociatedWith": { "items": { - "type": "string" + "$ref": "#/$defs/Agent" }, "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" - }, "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": { @@ -17781,11 +20051,10 @@ } }, "required": [ - "published_in", "id", "category" ], - "title": "JournalArticle", + "title": "LibraryPooling", "type": "object" }, "LifeStage": { @@ -17845,6 +20114,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -17926,6 +20202,13 @@ "rights": { "type": "string" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -18014,6 +20297,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -18647,6 +20937,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -18668,54 +20965,6 @@ "title": "Mammal", "type": "object" }, - "Mapping": { - "additionalProperties": false, - "description": "text", - "properties": { - "access_date": { - "type": "string" - }, - "authority": { - "type": "string" - }, - "creation_date": { - "type": "string" - }, - "gene_identifier_1": { - "type": "string" - }, - "gene_identifier_2": { - "type": "string" - }, - "member_of": { - "description": "Defines a mereological relation between a item and a collection.", - "items": { - "type": "string" - }, - "type": "array" - }, - "method": { - "type": "string" - } - }, - "title": "Mapping", - "type": "object" - }, - "Mappings": { - "additionalProperties": false, - "description": "A collection of mappings between identifiers", - "properties": { - "has_member": { - "description": "Defines a mereological relation between a collection and an item.", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "Mappings", - "type": "object" - }, "MaterialSample": { "additionalProperties": false, "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]", @@ -18762,6 +21011,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -19350,6 +21606,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -19998,6 +22261,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "trade_name": { "description": "", "type": "string" @@ -20103,10 +22373,17 @@ }, "type": "array" }, - "routes_of_delivery": { - "description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", + "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" + }, + "synonym": { + "description": "Alternate human-readable names for a thing", "items": { - "$ref": "#/$defs/DrugDeliveryEnum" + "type": "string" }, "type": "array" }, @@ -20187,6 +22464,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -20599,6 +22883,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "trade_name": { "description": "", "type": "string" @@ -20681,6 +22972,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -20851,6 +23149,13 @@ "rights": { "type": "string" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -20933,6 +23238,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -21016,6 +23328,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -21084,6 +23403,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -22326,6 +24652,13 @@ "description": "executive summary of a publication", "type": "string" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -22408,6 +24741,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "timepoint": { "description": "a point in time", "format": "time", @@ -22498,6 +24838,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -22597,6 +24944,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -22679,6 +25033,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "timepoint": { "description": "a point in time", "format": "time", @@ -22790,6 +25151,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -22867,6 +25235,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -22945,6 +25320,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -23027,6 +25409,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -23110,6 +25499,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -23178,6 +25574,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -23277,6 +25680,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -23344,6 +25754,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -23422,6 +25839,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -23500,6 +25924,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -23578,6 +26009,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -24053,6 +26491,13 @@ "description": "executive summary of a publication", "type": "string" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -24120,6 +26565,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -24228,6 +26680,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "trade_name": { "description": "", "type": "string" @@ -24402,6 +26861,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -24487,6 +26953,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -24685,6 +27158,13 @@ "description": "executive summary of a publication", "type": "string" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -25435,6 +27915,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -25517,6 +28004,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -25613,6 +28107,13 @@ "rights": { "type": "string" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -25712,6 +28213,13 @@ "rights": { "type": "string" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -26186,6 +28694,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -26307,6 +28822,13 @@ "description": "executive summary of a publication", "type": "string" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "description": "Should generally be set to an ontology class defined term for 'serial' or 'journal'.", "items": { @@ -26394,6 +28916,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -26416,6 +28945,15 @@ "title": "SeverityValue", "type": "object" }, + "SexType": { + "description": "", + "enum": [ + "female", + "male" + ], + "title": "SexType", + "type": "string" + }, "SiRNA": { "additionalProperties": false, "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.", @@ -26607,6 +29145,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "trade_name": { "description": "", "type": "string" @@ -26700,6 +29245,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -26782,6 +29334,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -26865,6 +29424,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "timepoint": { "description": "a point in time", "format": "time", @@ -26956,6 +29522,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -27034,6 +29607,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -27115,6 +29695,13 @@ "rights": { "type": "string" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -27405,6 +29992,13 @@ "rights": { "type": "string" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -27426,6 +30020,170 @@ "title": "TextMiningResult", "type": "object" }, + "TissueDissecting": { + "additionalProperties": false, + "description": "A process that takes a brain section and produces a tissue sample.", + "properties": { + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "pattern": "^biolink:[A-Z][A-Za-z]+$", + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "full_name": { + "description": "a long-form human readable name for a thing", + "type": "string" + }, + "generated": { + "items": { + "$ref": "#/$defs/TissueSample" + }, + "type": "array" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "type": "string" + }, + "name": { + "description": "A human-readable name for an attribute or entity.", + "type": "string" + }, + "provided_by": { + "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", + "items": { + "type": "string" + }, + "type": "array" + }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, + "type": { + "items": { + "type": "string" + }, + "type": "array" + }, + "used": { + "items": { + "$ref": "#/$defs/BrainSection" + }, + "type": "array" + }, + "wasAssociatedWith": { + "items": { + "$ref": "#/$defs/Agent" + }, + "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" + } + }, + "required": [ + "id", + "category" + ], + "title": "TissueDissecting", + "type": "object" + }, + "TissueSample": { + "additionalProperties": false, + "description": "", + "properties": { + "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.\n * In a neo4j database this MAY correspond to the neo4j label tag.\n * In an RDF database it should be a biolink model class URI.\nThis field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...\nIn an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", + "items": { + "type": "string" + }, + "type": "array" + }, + "description": { + "description": "a human-readable description of an entity", + "type": "string" + }, + "has_attribute": { + "description": "connects any entity to an attribute", + "items": { + "type": "string" + }, + "type": "array" + }, + "id": { + "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", + "type": "string" + }, + "iri": { + "description": "An IRI for an entity. This is determined by the id using expansion rules.", + "type": "string" + }, + "name": { + "description": "A human-readable name for an attribute or entity.", + "type": "string" + }, + "roi_label": { + "description": "The label of the region of interest.", + "type": "string" + }, + "roi_plan": { + "type": "string" + }, + "type": { + "items": { + "type": "string" + }, + "type": "array" + }, + "wasAttributedTo": { + "items": { + "$ref": "#/$defs/Agent" + }, + "type": "array" + }, + "wasDerivedFrom": { + "items": { + "$ref": "#/$defs/BrainSection" + }, + "type": "array" + }, + "wasGeneratedBy": { + "items": { + "$ref": "#/$defs/TissueDissecting" + }, + "type": "array" + } + }, + "required": [ + "id" + ], + "title": "TissueSample", + "type": "object" + }, "Transcript": { "additionalProperties": false, "description": "An RNA synthesized on a DNA or RNA template by an RNA polymerase.", @@ -27513,6 +30271,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "trade_name": { "description": "", "type": "string" @@ -27784,6 +30549,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -27872,6 +30644,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "timepoint": { "description": "a point in time", "format": "time", @@ -29156,6 +31935,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -29234,6 +32020,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -29347,6 +32140,13 @@ "description": "executive summary of a publication", "type": "string" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" @@ -29429,6 +32229,13 @@ }, "type": "array" }, + "synonym": { + "description": "Alternate human-readable names for a thing", + "items": { + "type": "string" + }, + "type": "array" + }, "type": { "items": { "type": "string" diff --git a/jsonld-context-autogen/kbmodel.context.jsonld b/jsonld-context-autogen/kbmodel.context.jsonld index 95ebeffd..781a0215 100644 --- a/jsonld-context-autogen/kbmodel.context.jsonld +++ b/jsonld-context-autogen/kbmodel.context.jsonld @@ -280,6 +280,7 @@ "@prefix": true }, "NBO-PROPERTY": "http://purl.obolibrary.org/obo/nbo#", + "NCBIAssembly": "https://www.ncbi.nlm.nih.gov/assembly/", "NCBIGene": "http://identifiers.org/ncbigene/", "NCBITaxon": { "@id": "http://purl.obolibrary.org/obo/NCBITaxon_", @@ -532,7 +533,7 @@ }, "ncats.drug": "https://drugs.ncats.io/drug/", "ncbi": { - "@id": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi", + "@id": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=", "@prefix": true }, "oboInOwl": "http://www.geneontology.org/formats/oboInOwl#", @@ -645,6 +646,12 @@ "@type": "@id", "@id": "biolink:amount_or_activity_increased_by" }, + "pcr_cycles": { + "@type": "xsd:integer" + }, + "percent_cdna_longer_than_400bp": { + "@type": "xsd:float" + }, "anatomical_context_qualifier": { "@id": "biolink:anatomical_context_qualifier" }, @@ -715,6 +722,9 @@ }, "@id": "biolink:available_from" }, + "avg_size_bp": { + "@type": "xsd:integer" + }, "base_coordinate": { "@type": "xsd:integer", "@id": "biolink:base_coordinate" @@ -730,10 +740,16 @@ "@type": "@id", "@id": "biolink:biomarker_for" }, + "birth_date": { + "@type": "xsd:date" + }, "bonferonni_adjusted_p_value": { "@type": "xsd:float", "@id": "biolink:bonferonni_adjusted_p_value" }, + "ordinal": { + "@type": "xsd:integer" + }, "broad_match": { "@type": "@id", "@id": "biolink:broad_match" @@ -899,6 +915,9 @@ "dataset_download_url": { "@id": "dcat:downloadURL" }, + "death_date": { + "@type": "xsd:date" + }, "decreased_amount_in": { "@type": "@id", "@id": "biolink:decreased_amount_in" @@ -967,6 +986,9 @@ "@type": "@id", "@id": "biolink:disrupts" }, + "num_cells_collected": { + "@type": "xsd:integer" + }, "distribution_download_url": { "@id": "biolink:distribution_download_url" }, @@ -1080,11 +1102,9 @@ "@type": "@id", "@id": "biolink:gene_fusion_with" }, - "gene_identifier_1": { - "@type": "@id" - }, - "gene_identifier_2": { - "@type": "@id" + "generated": { + "@type": "@id", + "@id": "prov:generated" }, "genetic_association": { "@type": "@id", @@ -1179,7 +1199,7 @@ }, "has_dataset": { "@type": "@id", - "@id": "dct:source" + "@id": "biolink:has_dataset" }, "has_decreased_amount": { "@type": "@id", @@ -1477,7 +1497,10 @@ "@id": "biolink:indirectly_physically_interacts_with" }, "ingest_date": { - "@id": "pav:version" + "@id": "biolink:ingest_date" + }, + "input_quantity": { + "@type": "xsd:float" }, "interacting_molecules_category": { "@type": "@id", @@ -1607,6 +1630,18 @@ "@type": "xsd:float", "@id": "biolink:latitude" }, + "quantification_fmol": { + "@type": "xsd:float" + }, + "quantification_ng": { + "@type": "xsd:float" + }, + "quantification_nm": { + "@type": "xsd:float" + }, + "tube_contents": { + "@type": "xsd:float" + }, "license": { "@id": "biolink:license" }, @@ -1685,6 +1720,9 @@ "@type": "@id", "@id": "biolink:mesh_terms" }, + "method": { + "@id": "schema:name" + }, "missing_from": { "@type": "@id", "@id": "biolink:missing_from" @@ -1918,6 +1956,9 @@ "primary_knowledge_source": { "@id": "biolink:primary_knowledge_source" }, + "process_pass": { + "@type": "xsd:boolean" + }, "produced_by": { "@type": "@id", "@id": "biolink:produced_by" @@ -2090,6 +2131,10 @@ "@type": "@id", "@id": "biolink:same_as" }, + "semmed_agreement_count": { + "@type": "xsd:integer", + "@id": "biolink:semmed_agreement_count" + }, "sensitivity_associated_with": { "@type": "@id", "@id": "biolink:sensitivity_associated_with" @@ -2109,6 +2154,14 @@ "@type": "@id", "@id": "biolink:severity_qualifier" }, + "sex": { + "@context": { + "@vocab": "@null", + "text": "skos:notation", + "description": "skos:prefLabel", + "meaning": "@id" + } + }, "sex_qualifier": { "@type": "@id", "@id": "biolink:sex_qualifier" @@ -2344,6 +2397,10 @@ "@type": "@id", "@id": "biolink:upstream_resource_ids" }, + "used": { + "@type": "@id", + "@id": "prov:used" + }, "variant_part_of": { "@type": "@id", "@id": "biolink:variant_part_of" @@ -2358,6 +2415,22 @@ "volume": { "@id": "biolink:volume" }, + "wasAssociatedWith": { + "@type": "@id", + "@id": "prov:wasAssociatedWith" + }, + "wasAttributedTo": { + "@type": "@id", + "@id": "prov:wasAttributedTo" + }, + "wasDerivedFrom": { + "@type": "@id", + "@id": "prov:wasDerivedFrom" + }, + "wasGeneratedBy": { + "@type": "@id", + "@id": "prov:wasGeneratedBy" + }, "xenologous_to": { "@type": "@id", "@id": "biolink:xenologous_to" diff --git a/linkml-schema/kbmodel.yaml b/linkml-schema/kbmodel.yaml index 7b295bc3..a9d9ab7d 100644 --- a/linkml-schema/kbmodel.yaml +++ b/linkml-schema/kbmodel.yaml @@ -6,7 +6,11 @@ prefixes: bican: https://identifiers.org/brain-bican/vocab/ spdx: http://spdx.org/rdf/terms# schema: http://schema.org/ - ncbi: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi + ncbi: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id= + NCBIAssembly: https://www.ncbi.nlm.nih.gov/assembly/ + prov: http://www.w3.org/ns/prov# + + imports: - linkml:types - biolink:biolink-model @@ -38,19 +42,17 @@ classes: - version - digest - content_url + - authority genome assembly: -# is_a: named thing -# mixins: -# - thing with taxon + is_a: named thing + mixins: + - thing with taxon description: >- Genome assembly to contain version and label information - attributes: - id: - taxon: - version: - label: - description: + slots: + - version + - strain checksum: is_a: entity @@ -58,28 +60,10 @@ classes: Checksum values associated with digital entities. slots: - checksum algorithm - - value - - mapping: - description: text - slots: - - gene_identifier_1 - - gene_identifier_2 - - authority - - method - - creation_date - - access_date - - member of - notes: relate to - https://mapping-commons.github.io/sssom/ - - - mappings: - description: > - A collection of mappings between identifiers - slots: - - has member - notes: use this model - https://mapping-commons.github.io/sssom/ - + attributes: + value: + description: The checksum value obtained from a specific cryotographic hash function. + annotation collection: tree_root: true attributes: @@ -96,34 +80,490 @@ classes: inlined_as_list: true range: genome assembly + prov activity: + mixin: true + description: >- + Based off prov:Activity; 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. + slots: + - used + - generated + - wasAssociatedWith + + + brain extraction: + description: >- + A process that takes a brain sample from a donor and produces a brain segment. + is_a: activity + mixins: + - prov activity + slot_usage: + used: + range: donor + generated: + range: brain segment + + brain segment sectioning: + description: >- + A process that takes a brain segment and produces a brain section. + is_a: activity + mixins: + - prov activity + slot_usage: + used: + range: brain segment + generated: + range: brain section + + tissue dissecting: + description: >- + A process that takes a brain section and produces a tissue sample. + is_a: activity + mixins: + - prov activity + slot_usage: + used: + range: brain section + generated: + range: tissue sample + + cell dissociation: + description: >- + A process that takes a tissue sample and produces a dissociated cell sample. + is_a: activity + mixins: + - prov activity + slot_usage: + used: + range: tissue sample + generated: + range: dissociated cell sample + + cell enrichment: + description: >- + A process that takes a dissociated cell sample and produces an enriched cell sample. + is_a: activity + mixins: + - prov activity + slot_usage: + used: + range: dissociated cell sample + generated: + range: enriched cell sample + + cell barcoding: + description: >- + A process that takes an enriched cell sample and produces a barcoded cell sample. + is_a: activity + mixins: + - prov activity + slot_usage: + used: + range: enriched cell sample + generated: + range: barcoded cell sample + + cdna amplification: + description: >- + A process that takes a barcoded cell sample and produces an amplified cDNA sample. + is_a: activity + mixins: + - prov activity + slot_usage: + used: + range: barcoded cell sample + generated: + range: amplified cdna + + library construction: + description: >- + A process that takes an amplified cDNA sample and produces a library. + is_a: activity + mixins: + - prov activity + slot_usage: + used: + range: amplified cdna + generated: + range: library + + library aliquoting: + description: >- + A process that takes a library and produces an library aliquot. + is_a: activity + mixins: + - prov activity + slot_usage: + used: + range: library + generated: + range: library aliquot + + library pooling: + description: >- + A process that takes a library aliquot and produces a library pool. + is_a: activity + mixins: + - prov activity + slot_usage: + used: + range: library aliquot + generated: + range: library pool + + + prov entity: + mixin: true + description: >- + Based off prov:Entity; an entity is a physical, digital, conceptual, or other kind of thing with some fixed aspects; + entities may be real or imaginary. + slots: + - wasDerivedFrom + - wasGeneratedBy + - wasAttributedTo + + + # 028 - donors.ipynb + # age_at_death -> death age, date_of_birth -> birth date, date_of_death -> death date, full_genotype -> full genotype, + # entity_type -> type/category, label -> name, ncbitaxonomyid -> in_taxon, sex -> sex + donor: + is_a: agent + mixins: + - thing with taxon + description: >- + A person or organism that is the source of a biological sample. + slots: + - sex + - birth date + - death date + - death age + - full genotype + + + # 027 - brain_extraction.ipynb + # mappings (notebook -> model): anatomical_division -> anatomical division, barcode -> id, + # (created_by_process_id & created_by_process_type) -> wasGeneratedBy, entity_type -> type/category, label -> name + brain segment: + is_a: entity + mixins: + - prov entity + attributes: + anatomical division: + slot_usage: + wasGeneratedBy: + range: brain extraction + wasDerivedFrom: + range: donor + + + # 026 - brain_segment_sectioning.ipynb + # mappings (notebook -> model): barcode -> id, (created_by_process_id & created_by_process_type) -> wasGeneratedBy, + # entity_type -> type/category, label -> name, ordinal -> ordinal + brain section: + is_a: entity + mixins: + - prov entity + attributes: + ordinal: + description: The ordinal number of the section. + range: integer + slot_usage: + wasGeneratedBy: + range: brain segment sectioning + wasDerivedFrom: + range: brain segment + + + # 025b - tissue_dissectioning.ipynb + # mappings (notebook -> model): (created_by_process_id & created_by_process_type) -> wasGeneratedBy, entity_type -> type/category, + # label -> name, roi_plan -> roi plan, roi_label -> roi label + tissue sample: + is_a: entity + mixins: + - prov entity + attributes: + roi plan: + roi label: + description: The label of the region of interest. + slot_usage: + wasGeneratedBy: + range: tissue dissecting + wasDerivedFrom: + range: brain section + + + # 024 - cell_dissociation.ipynb + # mappings (notebook -> model): cell_prep_type -> cell prep type, (created_by_process_id & created_by_process_type) -> wasGeneratedBy, + # entity_type -> type/category, facs_population_plan -> facs population plan, label -> name, number_of_cells_collected -> num cells collected + dissociated cell sample: + is_a: entity + mixins: + - prov entity + attributes: + cell prep type: + facs population plan: + num cells collected: + range: integer + slot_usage: + wasGeneratedBy: + range: cell dissociation + wasDerivedFrom: + range: tissue sample + + + enriched cell sample: + is_a: entity + mixins: + - prov entity + slot_usage: + wasGeneratedBy: + range: cell enrichment + wasDerivedFrom: + range: dissociated cell sample + + + # 023 - cell_barcoding.ipynb + # mappings (notebook -> model): (created_by_process_id & created_by_process_type) -> wasGeneratedBy, entity_type -> type/category, + # label -> name, port_well -> port well, sample_quality_count -> sample quality count + barcoded cell sample: + is_a: entity + mixins: + - prov entity + attributes: + port well: + sample quality count: + slot_usage: + wasGeneratedBy: + range: cell barcoding + wasDerivedFrom: + range: enriched cell sample + + + # 022 - cnda_amplification.ipynb + # amplified_quantity_ng -> input quantity, (created_by_process_id & created_by_process_type) -> wasGeneratedBy, entity_type -> type/category, + # label -> name, method -> method, pcr_cycles -> pcr cycles, percent_cdna_longer_than_400bp -> percent cdna longer than 400bp, rna_amplification_pass_fail -> process pass + amplified cdna: + is_a: entity + mixins: + - prov entity + slots: + - method + - input quantity + - process pass + attributes: + pcr cycles: + description: >- + Number of PCR cycles used to amplify the cDNA. + range: integer + percent cdna longer than 400bp: + description: >- + The percentage of cDNA fragments that are longer than 400bp. + range: float + slot_usage: + input quantity: + description: The amount of input cDNA (ng) amplified. + process pass: + description: Indicates whether the rna amplification process passed or failed. + wasGeneratedBy: + range: cdna amplification + wasDerivedFrom: + range: barcoded cell sample + + + # 021 - library_constructions.ipynb + # avg_size_bp -> avg size bp, (created_by_process_id & created_by_process_type) -> wasGeneratedBy, entity_type -> type/category, label -> name, + # library_creation_date -> creation date, library_input_ng -> input quantity, method -> method, process_pass -> process pass, + # quantification_fmole -> quantification fmol, quantification_ng -> quantification ng, quantification_nm -> quantification nm, + # r1_index -> r1 index, r1_sequence -> r1 sequence, r2_index -> r2 index, r2_sequence -> r2 sequence + library: + is_a: entity + mixins: + - prov entity + slots: + - method + - creation date + - input quantity + - process pass + - avg size bp + attributes: + quantification fmol: + range: float + quantification ng: + range: float + quantification nm: + range: float + r1 index: + r1 sequence: + r2 index: + r2 sequence: + slot_usage: + creation date: + description: The date and time the object was created. + range: datetime + input quantity: + description: The amount of input material (ng) used to create the library. + process pass: + description: Indicates whether the library prep process passed or failed. + avg size bp: + description: The average size (bp) of the library fragments. + wasGeneratedBy: + range: library construction + wasDerivedFrom: + range: amplified cdna + + + # 020 - aliquoting_and_pooling.ipynb + # mappings (notebook -> model): label -> name, input_quantity_fmol -> input quantity, library_label -> xref, + # (created_by_process_id & created_by_process_type) -> wasGeneratedBy, entity_type -> type/category, + library aliquot: + is_a: entity + mixins: + - prov entity + slots: + - input quantity + slot_usage: + wasGeneratedBy: + range: library aliquoting + wasDerivedFrom: + range: library + input quantity: + description: The amount of input material (fmol) used to create the library aliquot. + range: integer + + + # 020 - aliquoting_and_pooling.ipynb + # mappings (notebook -> model): label -> name, tube_avg_size_bp -> avg size bp, tube_contents_nm -> tube contents nm, tube_internal_label -> xref, + # (created_by_process_id & created_by_process_type) -> wasGeneratedBy, entity_type -> type/category, + library pool: + is_a: entity + mixins: + - prov entity + slots: + - avg size bp + attributes: + tube contents: + description: The content concentration (nm). + range: float + slot_usage: + avg size bp: + description: The average size (bp) of the library fragments in the tube. + wasGeneratedBy: + range: library pooling + wasDerivedFrom: + range: library aliquot + + slots: + used: + slot_uri: prov:used + domain: activity + range: entity + multivalued: true + inlined_as_list: true + + generated: + slot_uri: prov:generated + domain: activity + range: entity + multivalued: true + inlined_as_list: true + + wasGeneratedBy: + slot_uri: prov:wasGeneratedBy + domain: entity + range: activity + multivalued: true + inlined_as_list: true + + wasDerivedFrom: + slot_uri: prov:wasDerivedFrom + domain: entity + range: entity + multivalued: true + inlined_as_list: true + + wasAssociatedWith: + slot_uri: prov:wasAssociatedWith + domain: activity + range: agent + multivalued: true + inlined_as_list: true + + wasAttributedTo: + slot_uri: prov:wasAttributedTo + domain: entity + range: agent + multivalued: true + inlined_as_list: true + referenced in: range: genome annotation + molecular type: range: BioType + reference assembly: range: uriorcurie + digest: + description: Stores checksum information. range: checksum multivalued: true required: true + content_url: slot_uri: schema:url multivalued: true - gene_identifier_1: - range: gene annotation - gene_identifier_2: - range: gene annotation + authority: - method: - creation_date: - access_date: + description: The organization responsible for publishing the data. + checksum algorithm: + description: The type of cryptographic hash function used to calculate the checksum value. range: DigestType - value: + source id: description: The authority specific identifier. slot_uri: schema:identifier + + strain: + description: The genetic variant or subtype of a species or organism. + + sex: + range: SexType + + birth date: + description: The date of birth of the donor. + range: date + + death date: + description: The date of death of the donor. + range: date + + death age: + description: The age of the donor at the time of death (ISO 8601 format). + range: string + + full genotype: + description: The full genotype of the donor. + range: string + + method: + description: + slot_uri: schema:name + + input quantity: + description: The amount of input material used for an activity. + range: float + + process pass: + description: Indicates whether the process passed or failed. + range: boolean + + avg size bp: + description: The average size (bp = base pairs) of an entity. + range: integer + enums: DigestType: @@ -135,6 +575,11 @@ enums: SHA256: meaning: spdx:checksumAlgorithm_sha256 + SexType: + permissible_values: + female: + male: + BioType: permissible_values: protein_coding: diff --git a/models_py-autogen/ccn2.py b/models_py-autogen/ccn2.py index 7660499f..ed41fbad 100644 --- a/models_py-autogen/ccn2.py +++ b/models_py-autogen/ccn2.py @@ -3,7 +3,6 @@ from enum import Enum from typing import List, Dict, Optional, Any, Union from pydantic import BaseModel as BaseModel, Field -from linkml_runtime.linkml_model import Decimal import sys if sys.version_info >= (3, 8): from typing import Literal @@ -53,7 +52,6 @@ class Taxonomy(ConfiguredBaseModel): rank: Optional[Rank] = Field(None, description="""Algorithmically generated hierarchical taxonomies can be complex, with many nodes between root and leaf and branches of variable depth. To simplify this for display and discussion it can be useful to assign nodes to a 3 level hierarchy, with leaf nodes at the bottom.""") - class CrossTaxonomyMapping(ConfiguredBaseModel): cell_set_accession: str = Field(..., description="""Primary identifier for cell set.""") @@ -65,7 +63,6 @@ class CrossTaxonomyMapping(ConfiguredBaseModel): provenance: Optional[str] = Field(None, description="""ORCID of the person doing the mapping using the syntax ORCID:0123-4567-890. Optionally include supporting publications using DOIs of the form doi:10.1126/journal.abj6641.""") - class LocationMapping(ConfiguredBaseModel): cell_set_accession: str = Field(..., description="""Primary identifier for cell set.""") @@ -77,7 +74,6 @@ class LocationMapping(ConfiguredBaseModel): provenance: str = Field(..., description="""ORCID of the person doing the mapping using the syntax ORCID:0123-4567-890. Optionally include supporting publications using DOIs of the form doi:10.1126/journal.abj6641.""") - class CellSetAccessionToCellMapping(ConfiguredBaseModel): sample: str = Field(..., description="""Cell sample identifier.""") @@ -85,7 +81,6 @@ class CellSetAccessionToCellMapping(ConfiguredBaseModel): - # Update forward refs # see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ Taxonomy.update_forward_refs() diff --git a/models_py-autogen/figure1.py b/models_py-autogen/figure1.py index f626122a..1c15a273 100644 --- a/models_py-autogen/figure1.py +++ b/models_py-autogen/figure1.py @@ -3,7 +3,6 @@ from enum import Enum from typing import List, Dict, Optional, Any, Union from pydantic import BaseModel as BaseModel, Field -from linkml_runtime.linkml_model import Decimal import sys if sys.version_info >= (3, 8): from typing import Literal @@ -127,7 +126,6 @@ class NamedThing(ConfiguredBaseModel): label: Optional[str] = Field(None) - class CellClass(NamedThing): """ Class division in Figure 1, also found in Supplementary Materials: Table 7 @@ -138,7 +136,6 @@ class CellClass(NamedThing): label: Optional[str] = Field(None) - class CellSubclass(NamedThing): """ Subclass division in Figure 1 @@ -150,7 +147,6 @@ class CellSubclass(NamedThing): label: Optional[str] = Field(None) - class Cluster(NamedThing): """ Cluster in Supplementary Materials: Table 7 @@ -161,7 +157,6 @@ class Cluster(NamedThing): label: Optional[str] = Field(None) - class Cell(NamedThing): """ Cell, a member of a cluster @@ -172,27 +167,23 @@ class Cell(NamedThing): label: Optional[str] = Field(None) - class Relationship(ConfiguredBaseModel): related_to: str = Field(...) - class HierarchicalRelationship(Relationship): relationship_type: Optional[HierarchicalRelationshipType] = Field(None) related_to: str = Field(...) - class GroupRelationship(Relationship): relationship_type: Optional[GroupRelationshipType] = Field(None) related_to: str = Field(...) - class Container(ConfiguredBaseModel): subclasses: Optional[List[CellSubclass]] = Field(default_factory=list) @@ -202,7 +193,6 @@ class Container(ConfiguredBaseModel): - # Update forward refs # see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ NamedThing.update_forward_refs() diff --git a/models_py-autogen/kbmodel.py b/models_py-autogen/kbmodel.py index 52afde16..cec823e9 100644 --- a/models_py-autogen/kbmodel.py +++ b/models_py-autogen/kbmodel.py @@ -3,7 +3,6 @@ from enum import Enum from typing import List, Dict, Optional, Any, Union from pydantic import BaseModel as BaseModel, Field -from linkml_runtime.linkml_model import Decimal import sys if sys.version_info >= (3, 8): from typing import Literal @@ -38,6 +37,15 @@ class DigestType(str, Enum): +class SexType(str, Enum): + + + female = "female" + + male = "male" + + + class BioType(str, Enum): @@ -149,6 +157,10 @@ class GeneOrGeneProductOrChemicalEntityAspectEnum(str, Enum): uptake = "uptake" + splicing = "splicing" + + molecular_interaction = "molecular_interaction" + molecular_modification = "molecular_modification" acetylation = "acetylation" @@ -426,49 +438,31 @@ class FDAIDAAdverseEventEnum(str, Enum): -class GenomeAssembly(ConfiguredBaseModel): - """ - Genome assembly to contain version and label information - """ - id: Optional[str] = Field(None) - taxon: Optional[str] = Field(None) - version: Optional[str] = Field(None) - label: Optional[str] = Field(None) - description: Optional[str] = Field(None) +class AnnotationCollection(ConfiguredBaseModel): + + annotations: Optional[List[GeneAnnotation]] = Field(default_factory=list) + genome_annotations: Optional[List[GenomeAnnotation]] = Field(default_factory=list) + genome_assemblies: Optional[List[GenomeAssembly]] = Field(default_factory=list) - -class Mapping(ConfiguredBaseModel): +class ProvActivity(ConfiguredBaseModel): """ - text + Based off prov:Activity; 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. """ - gene_identifier_1: Optional[str] = Field(None) - gene_identifier_2: Optional[str] = Field(None) - authority: Optional[str] = Field(None) - method: Optional[str] = Field(None) - creation_date: Optional[str] = Field(None) - access_date: Optional[str] = Field(None) - member_of: Optional[List[str]] = Field(None, description="""Defines a mereological relation between a item and a collection.""") + used: Optional[List[Union[Entity,Checksum,BrainSegment,BrainSection,TissueSample,DissociatedCellSample,EnrichedCellSample,BarcodedCellSample,AmplifiedCdna,Library,LibraryAliquot,LibraryPool,NamedThing,Association,ChemicalEntityAssessesNamedThingAssociation,ContributorAssociation,GenotypeToGenotypePartAssociation,GenotypeToGeneAssociation,GenotypeToVariantAssociation,GeneToGeneAssociation,GeneToGeneFamilyAssociation,CellLineToDiseaseOrPhenotypicFeatureAssociation,ChemicalToChemicalAssociation,ChemicalToDiseaseOrPhenotypicFeatureAssociation,ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation,GeneToPathwayAssociation,MolecularActivityToPathwayAssociation,ChemicalToPathwayAssociation,NamedThingAssociatedWithLikelihoodOfNamedThingAssociation,ChemicalGeneInteractionAssociation,ChemicalAffectsGeneAssociation,DrugToGeneAssociation,MaterialSampleDerivationAssociation,MaterialSampleToDiseaseOrPhenotypicFeatureAssociation,DiseaseToExposureEventAssociation,ExposureEventToOutcomeAssociation,InformationContentEntityToNamedThingAssociation,DiseaseOrPhenotypicFeatureToLocationAssociation,DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation,GenotypeToPhenotypicFeatureAssociation,ExposureEventToPhenotypicFeatureAssociation,DiseaseToPhenotypicFeatureAssociation,CaseToPhenotypicFeatureAssociation,BehaviorToBehavioralFeatureAssociation,GeneToDiseaseOrPhenotypicFeatureAssociation,VariantToGeneAssociation,VariantToPopulationAssociation,PopulationToPopulationAssociation,VariantToPhenotypicFeatureAssociation,VariantToDiseaseAssociation,GenotypeToDiseaseAssociation,OrganismalEntityAsAModelOfDiseaseAssociation,OrganismToOrganismAssociation,TaxonToTaxonAssociation,GeneToExpressionSiteAssociation,SequenceVariantModulatesTreatmentAssociation,FunctionalAssociation,MolecularActivityToChemicalEntityAssociation,MolecularActivityToMolecularActivityAssociation,EntityToDiseaseAssociation,EntityToPhenotypicFeatureAssociation,SequenceAssociation,SequenceFeatureRelationship,ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation,AnatomicalEntityToAnatomicalEntityAssociation,OrganismTaxonToOrganismTaxonAssociation,OrganismTaxonToEnvironmentAssociation,OrganismTaxonToOrganismTaxonSpecialization,OrganismTaxonToOrganismTaxonInteraction,AnatomicalEntityToAnatomicalEntityPartOfAssociation,AnatomicalEntityToAnatomicalEntityOntogenicAssociation,TranscriptToGeneRelationship,GeneToGeneProductRelationship,ExonToTranscriptRelationship,GenomicSequenceLocalization,MacromolecularMachineToMolecularActivityAssociation,MacromolecularMachineToBiologicalProcessAssociation,MacromolecularMachineToCellularComponentAssociation,GeneToGoTermAssociation,GenotypeAsAModelOfDiseaseAssociation,VariantAsAModelOfDiseaseAssociation,VariantToGeneExpressionAssociation,GeneToPhenotypicFeatureAssociation,GeneToDiseaseAssociation,CausalGeneToDiseaseAssociation,CorrelatedGeneToDiseaseAssociation,DruggableGeneToDiseaseAssociation,GeneAsAModelOfDiseaseAssociation,GeneHasVariantThatContributesToDiseaseAssociation,ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation,ReactionToParticipantAssociation,ChemicalToChemicalDerivationAssociation,ReactionToCatalystAssociation,CellLineAsAModelOfDiseaseAssociation,GeneToGeneHomologyAssociation,GeneToGeneCoexpressionAssociation,PairwiseGeneToGeneInteraction,PairwiseMolecularInteraction,GenomeAssembly,Attribute,OrganismTaxon,Event,AdministrativeEntity,InformationContentEntity,PhysicalEntity,Activity,Procedure,Phenomenon,Device,DiagnosticAid,PlanetaryEntity,BiologicalEntity,ChemicalEntity,ClinicalEntity,Treatment,ClinicalTrial,ClinicalIntervention,Hospitalization,MolecularEntity,ChemicalMixture,EnvironmentalFoodContaminant,FoodAdditive,MolecularMixture,ComplexMolecularMixture,ProcessedMaterial,Food,Drug,SmallMolecule,NucleicAcidEntity,Exon,Transcript,CodingSequence,RNAProduct,RNAProductIsoform,NoncodingRNAProduct,MicroRNA,SiRNA,RegulatoryRegion,BiologicalProcessOrActivity,GeneticInheritance,OrganismalEntity,DiseaseOrPhenotypicFeature,Gene,MacromolecularComplex,NucleosomeModification,Genome,Polypeptide,ProteinDomain,PosttranslationalModification,ProteinFamily,NucleicAcidSequenceMotif,GeneFamily,Genotype,Haplotype,SequenceVariant,ReagentTargetedGene,Snv,Protein,ProteinIsoform,GenomeAnnotation,GeneAnnotation,Disease,PhenotypicFeature,BehavioralFeature,ClinicalFinding,Bacterium,Virus,CellularOrganism,LifeStage,IndividualOrganism,PopulationOfIndividualOrganisms,AnatomicalEntity,CellLine,CellularComponent,Cell,GrossAnatomicalStructure,PathologicalAnatomicalStructure,StudyPopulation,Cohort,Case,Mammal,Plant,Invertebrate,Vertebrate,Fungus,Human,MolecularActivity,BiologicalProcess,Pathway,PhysiologicalProcess,Behavior,PathologicalProcess,AccessibleDnaRegion,TranscriptionFactorBindingSite,EnvironmentalProcess,EnvironmentalFeature,GeographicLocation,GeographicLocationAtTime,BrainExtraction,BrainSegmentSectioning,TissueDissecting,CellDissociation,CellEnrichment,CellBarcoding,CdnaAmplification,LibraryConstruction,LibraryAliquoting,LibraryPooling,Study,MaterialSample,StudyResult,StudyVariable,CommonDataElement,Dataset,DatasetDistribution,DatasetVersion,DatasetSummary,ConfidenceLevel,EvidenceType,Publication,RetrievalSource,Book,BookChapter,Serial,Article,Patent,WebPage,PreprintPublication,DrugLabel,JournalArticle,ConceptCountAnalysisResult,ObservedExpectedFrequencyAnalysisResult,RelativeFrequencyAnalysisResult,TextMiningResult,ChiSquaredAnalysisResult,LogOddsAnalysisResult,Agent,Donor,ChemicalRole,BiologicalSex,SeverityValue,OrganismAttribute,Zygosity,ClinicalAttribute,SocioeconomicAttribute,GenomicBackgroundExposure,PathologicalProcessExposure,PathologicalAnatomicalExposure,DiseaseOrPhenotypicFeatureExposure,ChemicalExposure,ComplexChemicalExposure,BioticExposure,EnvironmentalExposure,BehavioralExposure,SocioeconomicExposure,GeographicExposure,DrugExposure,DrugToGeneInteractionExposure,ClinicalMeasurement,ClinicalModifier,ClinicalCourse,Onset,PhenotypicQuality,PhenotypicSex,GenotypicSex]]] = Field(default_factory=list) + generated: Optional[List[Union[Entity,Checksum,BrainSegment,BrainSection,TissueSample,DissociatedCellSample,EnrichedCellSample,BarcodedCellSample,AmplifiedCdna,Library,LibraryAliquot,LibraryPool,NamedThing,Association,ChemicalEntityAssessesNamedThingAssociation,ContributorAssociation,GenotypeToGenotypePartAssociation,GenotypeToGeneAssociation,GenotypeToVariantAssociation,GeneToGeneAssociation,GeneToGeneFamilyAssociation,CellLineToDiseaseOrPhenotypicFeatureAssociation,ChemicalToChemicalAssociation,ChemicalToDiseaseOrPhenotypicFeatureAssociation,ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation,GeneToPathwayAssociation,MolecularActivityToPathwayAssociation,ChemicalToPathwayAssociation,NamedThingAssociatedWithLikelihoodOfNamedThingAssociation,ChemicalGeneInteractionAssociation,ChemicalAffectsGeneAssociation,DrugToGeneAssociation,MaterialSampleDerivationAssociation,MaterialSampleToDiseaseOrPhenotypicFeatureAssociation,DiseaseToExposureEventAssociation,ExposureEventToOutcomeAssociation,InformationContentEntityToNamedThingAssociation,DiseaseOrPhenotypicFeatureToLocationAssociation,DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation,GenotypeToPhenotypicFeatureAssociation,ExposureEventToPhenotypicFeatureAssociation,DiseaseToPhenotypicFeatureAssociation,CaseToPhenotypicFeatureAssociation,BehaviorToBehavioralFeatureAssociation,GeneToDiseaseOrPhenotypicFeatureAssociation,VariantToGeneAssociation,VariantToPopulationAssociation,PopulationToPopulationAssociation,VariantToPhenotypicFeatureAssociation,VariantToDiseaseAssociation,GenotypeToDiseaseAssociation,OrganismalEntityAsAModelOfDiseaseAssociation,OrganismToOrganismAssociation,TaxonToTaxonAssociation,GeneToExpressionSiteAssociation,SequenceVariantModulatesTreatmentAssociation,FunctionalAssociation,MolecularActivityToChemicalEntityAssociation,MolecularActivityToMolecularActivityAssociation,EntityToDiseaseAssociation,EntityToPhenotypicFeatureAssociation,SequenceAssociation,SequenceFeatureRelationship,ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation,AnatomicalEntityToAnatomicalEntityAssociation,OrganismTaxonToOrganismTaxonAssociation,OrganismTaxonToEnvironmentAssociation,OrganismTaxonToOrganismTaxonSpecialization,OrganismTaxonToOrganismTaxonInteraction,AnatomicalEntityToAnatomicalEntityPartOfAssociation,AnatomicalEntityToAnatomicalEntityOntogenicAssociation,TranscriptToGeneRelationship,GeneToGeneProductRelationship,ExonToTranscriptRelationship,GenomicSequenceLocalization,MacromolecularMachineToMolecularActivityAssociation,MacromolecularMachineToBiologicalProcessAssociation,MacromolecularMachineToCellularComponentAssociation,GeneToGoTermAssociation,GenotypeAsAModelOfDiseaseAssociation,VariantAsAModelOfDiseaseAssociation,VariantToGeneExpressionAssociation,GeneToPhenotypicFeatureAssociation,GeneToDiseaseAssociation,CausalGeneToDiseaseAssociation,CorrelatedGeneToDiseaseAssociation,DruggableGeneToDiseaseAssociation,GeneAsAModelOfDiseaseAssociation,GeneHasVariantThatContributesToDiseaseAssociation,ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation,ReactionToParticipantAssociation,ChemicalToChemicalDerivationAssociation,ReactionToCatalystAssociation,CellLineAsAModelOfDiseaseAssociation,GeneToGeneHomologyAssociation,GeneToGeneCoexpressionAssociation,PairwiseGeneToGeneInteraction,PairwiseMolecularInteraction,GenomeAssembly,Attribute,OrganismTaxon,Event,AdministrativeEntity,InformationContentEntity,PhysicalEntity,Activity,Procedure,Phenomenon,Device,DiagnosticAid,PlanetaryEntity,BiologicalEntity,ChemicalEntity,ClinicalEntity,Treatment,ClinicalTrial,ClinicalIntervention,Hospitalization,MolecularEntity,ChemicalMixture,EnvironmentalFoodContaminant,FoodAdditive,MolecularMixture,ComplexMolecularMixture,ProcessedMaterial,Food,Drug,SmallMolecule,NucleicAcidEntity,Exon,Transcript,CodingSequence,RNAProduct,RNAProductIsoform,NoncodingRNAProduct,MicroRNA,SiRNA,RegulatoryRegion,BiologicalProcessOrActivity,GeneticInheritance,OrganismalEntity,DiseaseOrPhenotypicFeature,Gene,MacromolecularComplex,NucleosomeModification,Genome,Polypeptide,ProteinDomain,PosttranslationalModification,ProteinFamily,NucleicAcidSequenceMotif,GeneFamily,Genotype,Haplotype,SequenceVariant,ReagentTargetedGene,Snv,Protein,ProteinIsoform,GenomeAnnotation,GeneAnnotation,Disease,PhenotypicFeature,BehavioralFeature,ClinicalFinding,Bacterium,Virus,CellularOrganism,LifeStage,IndividualOrganism,PopulationOfIndividualOrganisms,AnatomicalEntity,CellLine,CellularComponent,Cell,GrossAnatomicalStructure,PathologicalAnatomicalStructure,StudyPopulation,Cohort,Case,Mammal,Plant,Invertebrate,Vertebrate,Fungus,Human,MolecularActivity,BiologicalProcess,Pathway,PhysiologicalProcess,Behavior,PathologicalProcess,AccessibleDnaRegion,TranscriptionFactorBindingSite,EnvironmentalProcess,EnvironmentalFeature,GeographicLocation,GeographicLocationAtTime,BrainExtraction,BrainSegmentSectioning,TissueDissecting,CellDissociation,CellEnrichment,CellBarcoding,CdnaAmplification,LibraryConstruction,LibraryAliquoting,LibraryPooling,Study,MaterialSample,StudyResult,StudyVariable,CommonDataElement,Dataset,DatasetDistribution,DatasetVersion,DatasetSummary,ConfidenceLevel,EvidenceType,Publication,RetrievalSource,Book,BookChapter,Serial,Article,Patent,WebPage,PreprintPublication,DrugLabel,JournalArticle,ConceptCountAnalysisResult,ObservedExpectedFrequencyAnalysisResult,RelativeFrequencyAnalysisResult,TextMiningResult,ChiSquaredAnalysisResult,LogOddsAnalysisResult,Agent,Donor,ChemicalRole,BiologicalSex,SeverityValue,OrganismAttribute,Zygosity,ClinicalAttribute,SocioeconomicAttribute,GenomicBackgroundExposure,PathologicalProcessExposure,PathologicalAnatomicalExposure,DiseaseOrPhenotypicFeatureExposure,ChemicalExposure,ComplexChemicalExposure,BioticExposure,EnvironmentalExposure,BehavioralExposure,SocioeconomicExposure,GeographicExposure,DrugExposure,DrugToGeneInteractionExposure,ClinicalMeasurement,ClinicalModifier,ClinicalCourse,Onset,PhenotypicQuality,PhenotypicSex,GenotypicSex]]] = Field(default_factory=list) + wasAssociatedWith: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) - -class Mappings(ConfiguredBaseModel): +class ProvEntity(ConfiguredBaseModel): """ - A collection of mappings between identifiers - + Based off prov:Entity; an entity is a physical, digital, conceptual, or other kind of thing with some fixed aspects; entities may be real or imaginary. """ - has_member: Optional[List[str]] = Field(None, description="""Defines a mereological relation between a collection and an item.""") - - - -class AnnotationCollection(ConfiguredBaseModel): - - annotations: Optional[List[GeneAnnotation]] = Field(default_factory=list) - genome_annotations: Optional[List[GenomeAnnotation]] = Field(default_factory=list) - genome_assemblies: Optional[List[GenomeAssembly]] = Field(default_factory=list) + wasDerivedFrom: Optional[List[Union[Entity,Checksum,BrainSegment,BrainSection,TissueSample,DissociatedCellSample,EnrichedCellSample,BarcodedCellSample,AmplifiedCdna,Library,LibraryAliquot,LibraryPool,NamedThing,Association,ChemicalEntityAssessesNamedThingAssociation,ContributorAssociation,GenotypeToGenotypePartAssociation,GenotypeToGeneAssociation,GenotypeToVariantAssociation,GeneToGeneAssociation,GeneToGeneFamilyAssociation,CellLineToDiseaseOrPhenotypicFeatureAssociation,ChemicalToChemicalAssociation,ChemicalToDiseaseOrPhenotypicFeatureAssociation,ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation,GeneToPathwayAssociation,MolecularActivityToPathwayAssociation,ChemicalToPathwayAssociation,NamedThingAssociatedWithLikelihoodOfNamedThingAssociation,ChemicalGeneInteractionAssociation,ChemicalAffectsGeneAssociation,DrugToGeneAssociation,MaterialSampleDerivationAssociation,MaterialSampleToDiseaseOrPhenotypicFeatureAssociation,DiseaseToExposureEventAssociation,ExposureEventToOutcomeAssociation,InformationContentEntityToNamedThingAssociation,DiseaseOrPhenotypicFeatureToLocationAssociation,DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation,GenotypeToPhenotypicFeatureAssociation,ExposureEventToPhenotypicFeatureAssociation,DiseaseToPhenotypicFeatureAssociation,CaseToPhenotypicFeatureAssociation,BehaviorToBehavioralFeatureAssociation,GeneToDiseaseOrPhenotypicFeatureAssociation,VariantToGeneAssociation,VariantToPopulationAssociation,PopulationToPopulationAssociation,VariantToPhenotypicFeatureAssociation,VariantToDiseaseAssociation,GenotypeToDiseaseAssociation,OrganismalEntityAsAModelOfDiseaseAssociation,OrganismToOrganismAssociation,TaxonToTaxonAssociation,GeneToExpressionSiteAssociation,SequenceVariantModulatesTreatmentAssociation,FunctionalAssociation,MolecularActivityToChemicalEntityAssociation,MolecularActivityToMolecularActivityAssociation,EntityToDiseaseAssociation,EntityToPhenotypicFeatureAssociation,SequenceAssociation,SequenceFeatureRelationship,ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation,AnatomicalEntityToAnatomicalEntityAssociation,OrganismTaxonToOrganismTaxonAssociation,OrganismTaxonToEnvironmentAssociation,OrganismTaxonToOrganismTaxonSpecialization,OrganismTaxonToOrganismTaxonInteraction,AnatomicalEntityToAnatomicalEntityPartOfAssociation,AnatomicalEntityToAnatomicalEntityOntogenicAssociation,TranscriptToGeneRelationship,GeneToGeneProductRelationship,ExonToTranscriptRelationship,GenomicSequenceLocalization,MacromolecularMachineToMolecularActivityAssociation,MacromolecularMachineToBiologicalProcessAssociation,MacromolecularMachineToCellularComponentAssociation,GeneToGoTermAssociation,GenotypeAsAModelOfDiseaseAssociation,VariantAsAModelOfDiseaseAssociation,VariantToGeneExpressionAssociation,GeneToPhenotypicFeatureAssociation,GeneToDiseaseAssociation,CausalGeneToDiseaseAssociation,CorrelatedGeneToDiseaseAssociation,DruggableGeneToDiseaseAssociation,GeneAsAModelOfDiseaseAssociation,GeneHasVariantThatContributesToDiseaseAssociation,ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation,ReactionToParticipantAssociation,ChemicalToChemicalDerivationAssociation,ReactionToCatalystAssociation,CellLineAsAModelOfDiseaseAssociation,GeneToGeneHomologyAssociation,GeneToGeneCoexpressionAssociation,PairwiseGeneToGeneInteraction,PairwiseMolecularInteraction,GenomeAssembly,Attribute,OrganismTaxon,Event,AdministrativeEntity,InformationContentEntity,PhysicalEntity,Activity,Procedure,Phenomenon,Device,DiagnosticAid,PlanetaryEntity,BiologicalEntity,ChemicalEntity,ClinicalEntity,Treatment,ClinicalTrial,ClinicalIntervention,Hospitalization,MolecularEntity,ChemicalMixture,EnvironmentalFoodContaminant,FoodAdditive,MolecularMixture,ComplexMolecularMixture,ProcessedMaterial,Food,Drug,SmallMolecule,NucleicAcidEntity,Exon,Transcript,CodingSequence,RNAProduct,RNAProductIsoform,NoncodingRNAProduct,MicroRNA,SiRNA,RegulatoryRegion,BiologicalProcessOrActivity,GeneticInheritance,OrganismalEntity,DiseaseOrPhenotypicFeature,Gene,MacromolecularComplex,NucleosomeModification,Genome,Polypeptide,ProteinDomain,PosttranslationalModification,ProteinFamily,NucleicAcidSequenceMotif,GeneFamily,Genotype,Haplotype,SequenceVariant,ReagentTargetedGene,Snv,Protein,ProteinIsoform,GenomeAnnotation,GeneAnnotation,Disease,PhenotypicFeature,BehavioralFeature,ClinicalFinding,Bacterium,Virus,CellularOrganism,LifeStage,IndividualOrganism,PopulationOfIndividualOrganisms,AnatomicalEntity,CellLine,CellularComponent,Cell,GrossAnatomicalStructure,PathologicalAnatomicalStructure,StudyPopulation,Cohort,Case,Mammal,Plant,Invertebrate,Vertebrate,Fungus,Human,MolecularActivity,BiologicalProcess,Pathway,PhysiologicalProcess,Behavior,PathologicalProcess,AccessibleDnaRegion,TranscriptionFactorBindingSite,EnvironmentalProcess,EnvironmentalFeature,GeographicLocation,GeographicLocationAtTime,BrainExtraction,BrainSegmentSectioning,TissueDissecting,CellDissociation,CellEnrichment,CellBarcoding,CdnaAmplification,LibraryConstruction,LibraryAliquoting,LibraryPooling,Study,MaterialSample,StudyResult,StudyVariable,CommonDataElement,Dataset,DatasetDistribution,DatasetVersion,DatasetSummary,ConfidenceLevel,EvidenceType,Publication,RetrievalSource,Book,BookChapter,Serial,Article,Patent,WebPage,PreprintPublication,DrugLabel,JournalArticle,ConceptCountAnalysisResult,ObservedExpectedFrequencyAnalysisResult,RelativeFrequencyAnalysisResult,TextMiningResult,ChiSquaredAnalysisResult,LogOddsAnalysisResult,Agent,Donor,ChemicalRole,BiologicalSex,SeverityValue,OrganismAttribute,Zygosity,ClinicalAttribute,SocioeconomicAttribute,GenomicBackgroundExposure,PathologicalProcessExposure,PathologicalAnatomicalExposure,DiseaseOrPhenotypicFeatureExposure,ChemicalExposure,ComplexChemicalExposure,BioticExposure,EnvironmentalExposure,BehavioralExposure,SocioeconomicExposure,GeographicExposure,DrugExposure,DrugToGeneInteractionExposure,ClinicalMeasurement,ClinicalModifier,ClinicalCourse,Onset,PhenotypicQuality,PhenotypicSex,GenotypicSex]]] = Field(default_factory=list) + wasGeneratedBy: Optional[List[Union[Activity,BrainExtraction,BrainSegmentSectioning,TissueDissecting,CellDissociation,CellEnrichment,CellBarcoding,CdnaAmplification,LibraryConstruction,LibraryAliquoting,LibraryPooling,Study]]] = Field(default_factory=list) + wasAttributedTo: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) - class MappingCollection(ConfiguredBaseModel): """ A collection of deprecated mappings. @@ -476,7 +470,6 @@ class MappingCollection(ConfiguredBaseModel): predicate_mappings: Optional[List[PredicateMapping]] = Field(None, description="""A collection of relationships that are not used in biolink, but have biolink patterns that can be used to replace them. This is a temporary slot to help with the transition to the fully qualified predicate model in Biolink3.""") - class PredicateMapping(ConfiguredBaseModel): """ A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place. @@ -504,7 +497,6 @@ class PredicateMapping(ConfiguredBaseModel): broad_match: Optional[List[str]] = Field(None, description="""a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree.""") - class OntologyClass(ConfiguredBaseModel): """ a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be considered both instances of biolink classes, and OWL classes in their own right. In general you should not need to use this class directly. Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess as the type. @@ -512,7 +504,6 @@ class OntologyClass(ConfiguredBaseModel): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") - class Annotation(ConfiguredBaseModel): """ Biolink Model root class for entity annotations. @@ -520,7 +511,6 @@ class Annotation(ConfiguredBaseModel): None - class QuantityValue(Annotation): """ A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value @@ -529,25 +519,21 @@ class QuantityValue(Annotation): has_numeric_value: Optional[float] = Field(None, description="""connects a quantity value to a number""") - class RelationshipQuantifier(ConfiguredBaseModel): None - class SensitivityQuantifier(RelationshipQuantifier): None - class SpecificityQuantifier(RelationshipQuantifier): None - class PathognomonicityQuantifier(SpecificityQuantifier): """ A relationship quantifier between a variant or symptom and a disease, which is high when the presence of the feature implies the existence of the disease @@ -555,7 +541,6 @@ class PathognomonicityQuantifier(SpecificityQuantifier): None - class FrequencyQuantifier(RelationshipQuantifier): has_count: Optional[int] = Field(None, description="""number of things with a particular property""") @@ -564,13 +549,11 @@ class FrequencyQuantifier(RelationshipQuantifier): has_percentage: Optional[float] = Field(None, description="""equivalent to has quotient multiplied by 100""") - class ChemicalOrDrugOrTreatment(ConfiguredBaseModel): None - class Entity(ConfiguredBaseModel): """ Root Biolink Model class for all things and informational relationships, real or imagined. @@ -588,13 +571,12 @@ class Entity(ConfiguredBaseModel): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class Checksum(Entity): """ Checksum values associated with digital entities. """ - checksum_algorithm: Optional[DigestType] = Field(None) - value: Optional[str] = Field(None) + checksum_algorithm: Optional[DigestType] = Field(None, description="""The type of cryptographic hash function used to calculate the checksum value.""") + value: Optional[str] = Field(None, description="""The checksum value obtained from a specific cryotographic hash function.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://identifiers.org/brain-bican/vocab/Checksum","bican:Checksum"]] = Field(["bican:Checksum"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -608,6 +590,214 @@ class Checksum(Entity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") +class BrainSegment(Entity, ProvEntity): + + anatomical_division: Optional[str] = Field(None) + wasDerivedFrom: Optional[List[Donor]] = Field(default_factory=list) + wasGeneratedBy: Optional[List[BrainExtraction]] = Field(default_factory=list) + wasAttributedTo: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://identifiers.org/brain-bican/vocab/BrainSegment","bican:BrainSegment"]] = Field(["bican:BrainSegment"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + +class BrainSection(Entity, ProvEntity): + + ordinal: Optional[int] = Field(None, description="""The ordinal number of the section.""") + wasDerivedFrom: Optional[List[BrainSegment]] = Field(default_factory=list) + wasGeneratedBy: Optional[List[BrainSegmentSectioning]] = Field(default_factory=list) + wasAttributedTo: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://identifiers.org/brain-bican/vocab/BrainSection","bican:BrainSection"]] = Field(["bican:BrainSection"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + +class TissueSample(Entity, ProvEntity): + + roi_plan: Optional[str] = Field(None) + roi_label: Optional[str] = Field(None, description="""The label of the region of interest.""") + wasDerivedFrom: Optional[List[BrainSection]] = Field(default_factory=list) + wasGeneratedBy: Optional[List[TissueDissecting]] = Field(default_factory=list) + wasAttributedTo: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://identifiers.org/brain-bican/vocab/TissueSample","bican:TissueSample"]] = Field(["bican:TissueSample"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + +class DissociatedCellSample(Entity, ProvEntity): + + cell_prep_type: Optional[str] = Field(None) + facs_population_plan: Optional[str] = Field(None) + num_cells_collected: Optional[int] = Field(None) + wasDerivedFrom: Optional[List[TissueSample]] = Field(default_factory=list) + wasGeneratedBy: Optional[List[CellDissociation]] = Field(default_factory=list) + wasAttributedTo: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://identifiers.org/brain-bican/vocab/DissociatedCellSample","bican:DissociatedCellSample"]] = Field(["bican:DissociatedCellSample"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + +class EnrichedCellSample(Entity, ProvEntity): + + wasDerivedFrom: Optional[List[DissociatedCellSample]] = Field(default_factory=list) + wasGeneratedBy: Optional[List[CellEnrichment]] = Field(default_factory=list) + wasAttributedTo: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://identifiers.org/brain-bican/vocab/EnrichedCellSample","bican:EnrichedCellSample"]] = Field(["bican:EnrichedCellSample"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + +class BarcodedCellSample(Entity, ProvEntity): + + port_well: Optional[str] = Field(None) + sample_quality_count: Optional[str] = Field(None) + wasDerivedFrom: Optional[List[EnrichedCellSample]] = Field(default_factory=list) + wasGeneratedBy: Optional[List[CellBarcoding]] = Field(default_factory=list) + wasAttributedTo: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://identifiers.org/brain-bican/vocab/BarcodedCellSample","bican:BarcodedCellSample"]] = Field(["bican:BarcodedCellSample"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + +class AmplifiedCdna(Entity, ProvEntity): + + method: Optional[str] = Field(None) + input_quantity: Optional[float] = Field(None, description="""The amount of input cDNA (ng) amplified.""") + process_pass: Optional[bool] = Field(None, description="""Indicates whether the rna amplification process passed or failed.""") + pcr_cycles: Optional[int] = Field(None, description="""Number of PCR cycles used to amplify the cDNA.""") + percent_cdna_longer_than_400bp: Optional[float] = Field(None, description="""The percentage of cDNA fragments that are longer than 400bp.""") + wasDerivedFrom: Optional[List[BarcodedCellSample]] = Field(default_factory=list) + wasGeneratedBy: Optional[List[CdnaAmplification]] = Field(default_factory=list) + wasAttributedTo: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://identifiers.org/brain-bican/vocab/AmplifiedCdna","bican:AmplifiedCdna"]] = Field(["bican:AmplifiedCdna"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + +class Library(Entity, ProvEntity): + + method: Optional[str] = Field(None) + creation_date: Optional[datetime ] = Field(None, description="""The date and time the object was created.""") + input_quantity: Optional[float] = Field(None, description="""The amount of input material (ng) used to create the library.""") + process_pass: Optional[bool] = Field(None, description="""Indicates whether the library prep process passed or failed.""") + avg_size_bp: Optional[int] = Field(None, description="""The average size (bp) of the library fragments.""") + quantification_fmol: Optional[float] = Field(None) + quantification_ng: Optional[float] = Field(None) + quantification_nm: Optional[float] = Field(None) + r1_index: Optional[str] = Field(None) + r1_sequence: Optional[str] = Field(None) + r2_index: Optional[str] = Field(None) + r2_sequence: Optional[str] = Field(None) + wasDerivedFrom: Optional[List[AmplifiedCdna]] = Field(default_factory=list) + wasGeneratedBy: Optional[List[LibraryConstruction]] = Field(default_factory=list) + wasAttributedTo: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://identifiers.org/brain-bican/vocab/Library","bican:Library"]] = Field(["bican:Library"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + +class LibraryAliquot(Entity, ProvEntity): + + input_quantity: Optional[int] = Field(None, description="""The amount of input material (fmol) used to create the library aliquot.""") + wasDerivedFrom: Optional[List[Library]] = Field(default_factory=list) + wasGeneratedBy: Optional[List[LibraryAliquoting]] = Field(default_factory=list) + wasAttributedTo: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://identifiers.org/brain-bican/vocab/LibraryAliquot","bican:LibraryAliquot"]] = Field(["bican:LibraryAliquot"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + +class LibraryPool(Entity, ProvEntity): + + avg_size_bp: Optional[int] = Field(None, description="""The average size (bp) of the library fragments in the tube.""") + tube_contents: Optional[float] = Field(None, description="""The content concentration (nm).""") + wasDerivedFrom: Optional[List[LibraryAliquot]] = Field(default_factory=list) + wasGeneratedBy: Optional[List[LibraryPooling]] = Field(default_factory=list) + wasAttributedTo: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://identifiers.org/brain-bican/vocab/LibraryPool","bican:LibraryPool"]] = Field(["bican:LibraryPool"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + class NamedThing(Entity): """ @@ -616,6 +806,7 @@ class NamedThing(Entity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/NamedThing","biolink:NamedThing"]] = Field(["biolink:NamedThing"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -629,7 +820,6 @@ class NamedThing(Entity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class Attribute(NamedThing, OntologyClass): """ A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material. @@ -643,6 +833,7 @@ class Attribute(NamedThing, OntologyClass): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/Attribute","biolink:Attribute"]] = Field(["biolink:Attribute"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -653,7 +844,6 @@ class Attribute(NamedThing, OntologyClass): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ChemicalRole(Attribute): """ A role played by the molecular entity or part thereof within a chemical context. @@ -667,6 +857,7 @@ class ChemicalRole(Attribute): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalRole","biolink:ChemicalRole"]] = Field(["biolink:ChemicalRole"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -677,7 +868,6 @@ class ChemicalRole(Attribute): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class BiologicalSex(Attribute): name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") @@ -689,6 +879,7 @@ class BiologicalSex(Attribute): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/BiologicalSex","biolink:BiologicalSex"]] = Field(["biolink:BiologicalSex"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -699,7 +890,6 @@ class BiologicalSex(Attribute): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class PhenotypicSex(BiologicalSex): """ An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present. @@ -713,6 +903,7 @@ class PhenotypicSex(BiologicalSex): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/PhenotypicSex","biolink:PhenotypicSex"]] = Field(["biolink:PhenotypicSex"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -723,7 +914,6 @@ class PhenotypicSex(BiologicalSex): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class GenotypicSex(BiologicalSex): """ An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes. @@ -737,6 +927,7 @@ class GenotypicSex(BiologicalSex): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/GenotypicSex","biolink:GenotypicSex"]] = Field(["biolink:GenotypicSex"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -747,7 +938,6 @@ class GenotypicSex(BiologicalSex): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class SeverityValue(Attribute): """ describes the severity of a phenotypic feature or disease @@ -761,6 +951,7 @@ class SeverityValue(Attribute): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/SeverityValue","biolink:SeverityValue"]] = Field(["biolink:SeverityValue"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -771,7 +962,6 @@ class SeverityValue(Attribute): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class RelationshipType(OntologyClass): """ An OWL property used as an edge label @@ -779,7 +969,6 @@ class RelationshipType(OntologyClass): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") - class TaxonomicRank(OntologyClass): """ A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom) @@ -787,7 +976,6 @@ class TaxonomicRank(OntologyClass): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") - class OrganismTaxon(NamedThing): """ A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies. @@ -795,6 +983,7 @@ class OrganismTaxon(NamedThing): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/OrganismTaxon","biolink:OrganismTaxon"]] = Field(["biolink:OrganismTaxon"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -808,7 +997,6 @@ class OrganismTaxon(NamedThing): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class Event(NamedThing): """ Something that happens at a given place and time. @@ -816,6 +1004,7 @@ class Event(NamedThing): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Event","biolink:Event"]] = Field(["biolink:Event"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -829,12 +1018,12 @@ class Event(NamedThing): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class AdministrativeEntity(NamedThing): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/AdministrativeEntity","biolink:AdministrativeEntity"]] = Field(["biolink:AdministrativeEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -848,7 +1037,6 @@ class AdministrativeEntity(NamedThing): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class Agent(AdministrativeEntity): """ person, group, organization or project that provides a piece of information (i.e. a knowledge association) @@ -858,6 +1046,7 @@ class Agent(AdministrativeEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Agent","biolink:Agent"]] = Field(["biolink:Agent"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -871,7 +1060,6 @@ class Agent(AdministrativeEntity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class InformationContentEntity(NamedThing): """ a piece of information that typically describes some topic of discourse or is used as support. @@ -883,6 +1071,7 @@ class InformationContentEntity(NamedThing): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/InformationContentEntity","biolink:InformationContentEntity"]] = Field(["biolink:InformationContentEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -896,7 +1085,6 @@ class InformationContentEntity(NamedThing): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class StudyResult(InformationContentEntity): """ A collection of data items from a study that are about a particular study subject or experimental unit (the 'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation of this data as evidence. @@ -908,6 +1096,7 @@ class StudyResult(InformationContentEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/StudyResult","biolink:StudyResult"]] = Field(["biolink:StudyResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -921,7 +1110,6 @@ class StudyResult(InformationContentEntity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class StudyVariable(InformationContentEntity): """ a variable that is used as a measure in the investigation of a study @@ -933,6 +1121,7 @@ class StudyVariable(InformationContentEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/StudyVariable","biolink:StudyVariable"]] = Field(["biolink:StudyVariable"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -946,7 +1135,6 @@ class StudyVariable(InformationContentEntity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class CommonDataElement(InformationContentEntity): """ A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different sites, studies, or clinical trials to ensure consistent data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. (https://cde.nlm.nih.gov/home) @@ -958,6 +1146,7 @@ class CommonDataElement(InformationContentEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CommonDataElement","biolink:CommonDataElement"]] = Field(["biolink:CommonDataElement"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -971,7 +1160,6 @@ class CommonDataElement(InformationContentEntity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ConceptCountAnalysisResult(StudyResult): """ A result of a concept count analysis. @@ -983,6 +1171,7 @@ class ConceptCountAnalysisResult(StudyResult): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ConceptCountAnalysisResult","biolink:ConceptCountAnalysisResult"]] = Field(["biolink:ConceptCountAnalysisResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -996,7 +1185,6 @@ class ConceptCountAnalysisResult(StudyResult): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ObservedExpectedFrequencyAnalysisResult(StudyResult): """ A result of a observed expected frequency analysis. @@ -1008,6 +1196,7 @@ class ObservedExpectedFrequencyAnalysisResult(StudyResult): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ObservedExpectedFrequencyAnalysisResult","biolink:ObservedExpectedFrequencyAnalysisResult"]] = Field(["biolink:ObservedExpectedFrequencyAnalysisResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1021,7 +1210,6 @@ class ObservedExpectedFrequencyAnalysisResult(StudyResult): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class RelativeFrequencyAnalysisResult(StudyResult): """ A result of a relative frequency analysis. @@ -1033,6 +1221,7 @@ class RelativeFrequencyAnalysisResult(StudyResult): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/RelativeFrequencyAnalysisResult","biolink:RelativeFrequencyAnalysisResult"]] = Field(["biolink:RelativeFrequencyAnalysisResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1046,7 +1235,6 @@ class RelativeFrequencyAnalysisResult(StudyResult): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class TextMiningResult(StudyResult): """ A result of text mining. @@ -1058,6 +1246,7 @@ class TextMiningResult(StudyResult): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/TextMiningResult","biolink:TextMiningResult"]] = Field(["biolink:TextMiningResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1071,7 +1260,6 @@ class TextMiningResult(StudyResult): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ChiSquaredAnalysisResult(StudyResult): """ A result of a chi squared analysis. @@ -1083,6 +1271,7 @@ class ChiSquaredAnalysisResult(StudyResult): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChiSquaredAnalysisResult","biolink:ChiSquaredAnalysisResult"]] = Field(["biolink:ChiSquaredAnalysisResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1096,7 +1285,6 @@ class ChiSquaredAnalysisResult(StudyResult): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class LogOddsAnalysisResult(StudyResult): """ A result of a log odds ratio analysis. @@ -1108,6 +1296,7 @@ class LogOddsAnalysisResult(StudyResult): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/LogOddsAnalysisResult","biolink:LogOddsAnalysisResult"]] = Field(["biolink:LogOddsAnalysisResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1121,7 +1310,6 @@ class LogOddsAnalysisResult(StudyResult): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class Dataset(InformationContentEntity): """ an item that refers to a collection of data from a data source. @@ -1133,6 +1321,7 @@ class Dataset(InformationContentEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Dataset","biolink:Dataset"]] = Field(["biolink:Dataset"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1146,7 +1335,6 @@ class Dataset(InformationContentEntity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class DatasetDistribution(InformationContentEntity): """ an item that holds distribution level information about a dataset. @@ -1159,6 +1347,7 @@ class DatasetDistribution(InformationContentEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DatasetDistribution","biolink:DatasetDistribution"]] = Field(["biolink:DatasetDistribution"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1172,7 +1361,6 @@ class DatasetDistribution(InformationContentEntity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class DatasetVersion(InformationContentEntity): """ an item that holds version level information about a dataset. @@ -1187,6 +1375,7 @@ class DatasetVersion(InformationContentEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DatasetVersion","biolink:DatasetVersion"]] = Field(["biolink:DatasetVersion"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1200,7 +1389,6 @@ class DatasetVersion(InformationContentEntity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class DatasetSummary(InformationContentEntity): """ an item that holds summary level information about a dataset. @@ -1214,6 +1402,7 @@ class DatasetSummary(InformationContentEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DatasetSummary","biolink:DatasetSummary"]] = Field(["biolink:DatasetSummary"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1227,7 +1416,6 @@ class DatasetSummary(InformationContentEntity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ConfidenceLevel(InformationContentEntity): """ Level of confidence in a statement @@ -1239,6 +1427,7 @@ class ConfidenceLevel(InformationContentEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ConfidenceLevel","biolink:ConfidenceLevel"]] = Field(["biolink:ConfidenceLevel"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1252,7 +1441,6 @@ class ConfidenceLevel(InformationContentEntity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class EvidenceType(InformationContentEntity): """ Class of evidence that supports an association @@ -1264,6 +1452,7 @@ class EvidenceType(InformationContentEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/EvidenceType","biolink:EvidenceType"]] = Field(["biolink:EvidenceType"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1277,7 +1466,6 @@ class EvidenceType(InformationContentEntity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class Publication(InformationContentEntity): """ Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP). @@ -1294,6 +1482,7 @@ class Publication(InformationContentEntity): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Publication","biolink:Publication"]] = Field(["biolink:Publication"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1307,7 +1496,6 @@ class Publication(InformationContentEntity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class Book(Publication): """ This class may rarely be instantiated except if use cases of a given knowledge graph support its utility. @@ -1324,6 +1512,7 @@ class Book(Publication): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Books should have industry-standard identifier such as from ISBN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Book","biolink:Book"]] = Field(["biolink:Book"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1337,7 +1526,6 @@ class Book(Publication): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class BookChapter(Publication): published_in: str = Field(..., description="""The enclosing parent book containing the chapter should have industry-standard identifier from ISBN.""") @@ -1355,6 +1543,7 @@ class BookChapter(Publication): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/BookChapter","biolink:BookChapter"]] = Field(["biolink:BookChapter"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1368,7 +1557,6 @@ class BookChapter(Publication): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class Serial(Publication): """ This class may rarely be instantiated except if use cases of a given knowledge graph support its utility. @@ -1388,6 +1576,7 @@ class Serial(Publication): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Serials (journals) should have industry-standard identifier such as from ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Serial","biolink:Serial"]] = Field(["biolink:Serial"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1401,7 +1590,6 @@ class Serial(Publication): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class Article(Publication): """ a piece of writing on a particular topic presented as a stand-alone section of a larger publication @@ -1422,6 +1610,7 @@ class Article(Publication): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Article","biolink:Article"]] = Field(["biolink:Article"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1435,7 +1624,6 @@ class Article(Publication): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class JournalArticle(Article): """ an article, typically presenting results of research, that is published in an issue of a scientific journal. @@ -1456,6 +1644,7 @@ class JournalArticle(Article): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/JournalArticle","biolink:JournalArticle"]] = Field(["biolink:JournalArticle"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1469,7 +1658,6 @@ class JournalArticle(Article): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class Patent(Publication): """ a legal document granted by a patent issuing authority which confers upon the patenter the sole right to make, use and sell an invention for a set period of time. @@ -1486,6 +1674,7 @@ class Patent(Publication): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Patent","biolink:Patent"]] = Field(["biolink:Patent"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1499,7 +1688,6 @@ class Patent(Publication): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class WebPage(Publication): """ a document that is published according to World Wide Web standards, which may incorporate text, graphics, sound, and/or other features. @@ -1516,6 +1704,7 @@ class WebPage(Publication): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/WebPage","biolink:WebPage"]] = Field(["biolink:WebPage"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1529,7 +1718,6 @@ class WebPage(Publication): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class PreprintPublication(Publication): """ a document reresenting an early version of an author's original scholarly work, such as a research paper or a review, prior to formal peer review and publication in a peer-reviewed scholarly or scientific journal. @@ -1546,6 +1734,7 @@ class PreprintPublication(Publication): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PreprintPublication","biolink:PreprintPublication"]] = Field(["biolink:PreprintPublication"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1559,7 +1748,6 @@ class PreprintPublication(Publication): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class DrugLabel(Publication): """ a document accompanying a drug or its container that provides written, printed or graphic information about the drug, including drug contents, specific instructions or warnings for administration, storage and disposal instructions, etc. @@ -1576,6 +1764,7 @@ class DrugLabel(Publication): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DrugLabel","biolink:DrugLabel"]] = Field(["biolink:DrugLabel"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1589,7 +1778,6 @@ class DrugLabel(Publication): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class RetrievalSource(InformationContentEntity): """ Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved. @@ -1604,6 +1792,7 @@ class RetrievalSource(InformationContentEntity): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/RetrievalSource","biolink:RetrievalSource"]] = Field(["biolink:RetrievalSource"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1617,7 +1806,6 @@ class RetrievalSource(InformationContentEntity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class PhysicalEssenceOrOccurrent(ConfiguredBaseModel): """ Either a physical or processual entity. @@ -1625,7 +1813,6 @@ class PhysicalEssenceOrOccurrent(ConfiguredBaseModel): None - class PhysicalEssence(PhysicalEssenceOrOccurrent): """ Semantic mixin concept. Pertains to entities that have physical properties such as mass, volume, or charge. @@ -1633,7 +1820,6 @@ class PhysicalEssence(PhysicalEssenceOrOccurrent): None - class PhysicalEntity(PhysicalEssence, NamedThing): """ An entity that has material reality (a.k.a. physical essence). @@ -1641,6 +1827,7 @@ class PhysicalEntity(PhysicalEssence, NamedThing): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PhysicalEntity","biolink:PhysicalEntity"]] = Field(["biolink:PhysicalEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1654,7 +1841,6 @@ class PhysicalEntity(PhysicalEssence, NamedThing): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class Occurrent(PhysicalEssenceOrOccurrent): """ A processual entity. @@ -1662,7 +1848,6 @@ class Occurrent(PhysicalEssenceOrOccurrent): None - class ActivityAndBehavior(Occurrent): """ Activity or behavior of any independent integral living, organization or mechanical actor in the world @@ -1670,7 +1855,6 @@ class ActivityAndBehavior(Occurrent): None - class Activity(ActivityAndBehavior, NamedThing): """ An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities. @@ -1678,6 +1862,7 @@ class Activity(ActivityAndBehavior, NamedThing): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Activity","biolink:Activity"]] = Field(["biolink:Activity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1691,6 +1876,245 @@ class Activity(ActivityAndBehavior, NamedThing): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") +class BrainExtraction(Activity, ProvActivity): + """ + A process that takes a brain sample from a donor and produces a brain segment. + """ + used: Optional[List[Donor]] = Field(default_factory=list) + generated: Optional[List[BrainSegment]] = Field(default_factory=list) + wasAssociatedWith: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://identifiers.org/brain-bican/vocab/BrainExtraction","bican:BrainExtraction"]] = Field(["bican:BrainExtraction"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + +class BrainSegmentSectioning(Activity, ProvActivity): + """ + A process that takes a brain segment and produces a brain section. + """ + used: Optional[List[BrainSegment]] = Field(default_factory=list) + generated: Optional[List[BrainSection]] = Field(default_factory=list) + wasAssociatedWith: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://identifiers.org/brain-bican/vocab/BrainSegmentSectioning","bican:BrainSegmentSectioning"]] = Field(["bican:BrainSegmentSectioning"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + +class TissueDissecting(Activity, ProvActivity): + """ + A process that takes a brain section and produces a tissue sample. + """ + used: Optional[List[BrainSection]] = Field(default_factory=list) + generated: Optional[List[TissueSample]] = Field(default_factory=list) + wasAssociatedWith: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://identifiers.org/brain-bican/vocab/TissueDissecting","bican:TissueDissecting"]] = Field(["bican:TissueDissecting"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + +class CellDissociation(Activity, ProvActivity): + """ + A process that takes a tissue sample and produces a dissociated cell sample. + """ + used: Optional[List[TissueSample]] = Field(default_factory=list) + generated: Optional[List[DissociatedCellSample]] = Field(default_factory=list) + wasAssociatedWith: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://identifiers.org/brain-bican/vocab/CellDissociation","bican:CellDissociation"]] = Field(["bican:CellDissociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + +class CellEnrichment(Activity, ProvActivity): + """ + A process that takes a dissociated cell sample and produces an enriched cell sample. + """ + used: Optional[List[DissociatedCellSample]] = Field(default_factory=list) + generated: Optional[List[EnrichedCellSample]] = Field(default_factory=list) + wasAssociatedWith: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://identifiers.org/brain-bican/vocab/CellEnrichment","bican:CellEnrichment"]] = Field(["bican:CellEnrichment"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + +class CellBarcoding(Activity, ProvActivity): + """ + A process that takes an enriched cell sample and produces a barcoded cell sample. + """ + used: Optional[List[EnrichedCellSample]] = Field(default_factory=list) + generated: Optional[List[BarcodedCellSample]] = Field(default_factory=list) + wasAssociatedWith: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://identifiers.org/brain-bican/vocab/CellBarcoding","bican:CellBarcoding"]] = Field(["bican:CellBarcoding"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + +class CdnaAmplification(Activity, ProvActivity): + """ + A process that takes a barcoded cell sample and produces an amplified cDNA sample. + """ + used: Optional[List[BarcodedCellSample]] = Field(default_factory=list) + generated: Optional[List[AmplifiedCdna]] = Field(default_factory=list) + wasAssociatedWith: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://identifiers.org/brain-bican/vocab/CdnaAmplification","bican:CdnaAmplification"]] = Field(["bican:CdnaAmplification"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + +class LibraryConstruction(Activity, ProvActivity): + """ + A process that takes an amplified cDNA sample and produces a library. + """ + used: Optional[List[AmplifiedCdna]] = Field(default_factory=list) + generated: Optional[List[Library]] = Field(default_factory=list) + wasAssociatedWith: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://identifiers.org/brain-bican/vocab/LibraryConstruction","bican:LibraryConstruction"]] = Field(["bican:LibraryConstruction"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + +class LibraryAliquoting(Activity, ProvActivity): + """ + A process that takes a library and produces an library aliquot. + """ + used: Optional[List[Library]] = Field(default_factory=list) + generated: Optional[List[LibraryAliquot]] = Field(default_factory=list) + wasAssociatedWith: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://identifiers.org/brain-bican/vocab/LibraryAliquoting","bican:LibraryAliquoting"]] = Field(["bican:LibraryAliquoting"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + +class LibraryPooling(Activity, ProvActivity): + """ + A process that takes a library aliquot and produces a library pool. + """ + used: Optional[List[LibraryAliquot]] = Field(default_factory=list) + generated: Optional[List[LibraryPool]] = Field(default_factory=list) + wasAssociatedWith: Optional[List[Union[Agent,Donor]]] = Field(default_factory=list) + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://identifiers.org/brain-bican/vocab/LibraryPooling","bican:LibraryPooling"]] = Field(["bican:LibraryPooling"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + class Study(Activity): """ @@ -1699,6 +2123,7 @@ class Study(Activity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Study","biolink:Study"]] = Field(["biolink:Study"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1712,7 +2137,6 @@ class Study(Activity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class Procedure(ActivityAndBehavior, NamedThing): """ A series of actions conducted in a certain order or manner @@ -1720,6 +2144,7 @@ class Procedure(ActivityAndBehavior, NamedThing): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Procedure","biolink:Procedure"]] = Field(["biolink:Procedure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1733,7 +2158,6 @@ class Procedure(ActivityAndBehavior, NamedThing): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class Phenomenon(Occurrent, NamedThing): """ a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question @@ -1741,6 +2165,7 @@ class Phenomenon(Occurrent, NamedThing): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Phenomenon","biolink:Phenomenon"]] = Field(["biolink:Phenomenon"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1754,7 +2179,6 @@ class Phenomenon(Occurrent, NamedThing): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class Device(NamedThing): """ A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment @@ -1762,6 +2186,7 @@ class Device(NamedThing): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Device","biolink:Device"]] = Field(["biolink:Device"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1775,7 +2200,6 @@ class Device(NamedThing): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class DiagnosticAid(NamedThing): """ A device or substance used to help diagnose disease or injury @@ -1783,6 +2207,7 @@ class DiagnosticAid(NamedThing): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DiagnosticAid","biolink:DiagnosticAid"]] = Field(["biolink:DiagnosticAid"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1796,7 +2221,6 @@ class DiagnosticAid(NamedThing): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class SubjectOfInvestigation(ConfiguredBaseModel): """ An entity that has the role of being studied in an investigation, study, or experiment @@ -1804,7 +2228,6 @@ class SubjectOfInvestigation(ConfiguredBaseModel): None - class MaterialSample(SubjectOfInvestigation, PhysicalEntity): """ A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. [SIO] @@ -1812,6 +2235,7 @@ class MaterialSample(SubjectOfInvestigation, PhysicalEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MaterialSample","biolink:MaterialSample"]] = Field(["biolink:MaterialSample"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1825,7 +2249,6 @@ class MaterialSample(SubjectOfInvestigation, PhysicalEntity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class PlanetaryEntity(NamedThing): """ Any entity or process that exists at the level of the whole planet @@ -1833,6 +2256,7 @@ class PlanetaryEntity(NamedThing): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PlanetaryEntity","biolink:PlanetaryEntity"]] = Field(["biolink:PlanetaryEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1846,12 +2270,12 @@ class PlanetaryEntity(NamedThing): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class EnvironmentalProcess(PlanetaryEntity, Occurrent): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/EnvironmentalProcess","biolink:EnvironmentalProcess"]] = Field(["biolink:EnvironmentalProcess"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1865,12 +2289,12 @@ class EnvironmentalProcess(PlanetaryEntity, Occurrent): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class EnvironmentalFeature(PlanetaryEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/EnvironmentalFeature","biolink:EnvironmentalFeature"]] = Field(["biolink:EnvironmentalFeature"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1884,7 +2308,6 @@ class EnvironmentalFeature(PlanetaryEntity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class GeographicLocation(PlanetaryEntity): """ a location that can be described in lat/long coordinates @@ -1894,6 +2317,7 @@ class GeographicLocation(PlanetaryEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeographicLocation","biolink:GeographicLocation"]] = Field(["biolink:GeographicLocation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1907,7 +2331,6 @@ class GeographicLocation(PlanetaryEntity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class GeographicLocationAtTime(GeographicLocation): """ a location that can be described in lat/long coordinates, for a particular time @@ -1918,6 +2341,7 @@ class GeographicLocationAtTime(GeographicLocation): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeographicLocationAtTime","biolink:GeographicLocationAtTime"]] = Field(["biolink:GeographicLocationAtTime"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1931,7 +2355,6 @@ class GeographicLocationAtTime(GeographicLocation): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ThingWithTaxon(ConfiguredBaseModel): """ A mixin that can be used on any entity that can be taxonomically classified. This includes individual organisms; genes, their products and other molecular entities; body parts; biological processes @@ -1940,6 +2363,60 @@ class ThingWithTaxon(ConfiguredBaseModel): in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") +class GenomeAssembly(ThingWithTaxon, NamedThing): + """ + Genome assembly to contain version and label information + """ + version: Optional[str] = Field(None) + strain: Optional[str] = Field(None, description="""The genetic variant or subtype of a species or organism.""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://identifiers.org/brain-bican/vocab/GenomeAssembly","bican:GenomeAssembly"]] = Field(["bican:GenomeAssembly"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + + +class Donor(ThingWithTaxon, Agent): + """ + A person or organism that is the source of a biological sample. + """ + sex: Optional[SexType] = Field(None) + birth_date: Optional[date] = Field(None, description="""The date of birth of the donor.""") + death_date: Optional[date] = Field(None, description="""The date of death of the donor.""") + death_age: Optional[str] = Field(None, description="""The age of the donor at the time of death (ISO 8601 format).""") + full_genotype: Optional[str] = Field(None, description="""The full genotype of the donor.""") + in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") + in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") + affiliation: Optional[List[str]] = Field(default_factory=list, description="""a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations.""") + address: Optional[str] = Field(None, description="""the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?).""") + provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") + xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + id: str = Field(..., description="""Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code.""") + iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") + category: List[Literal["https://identifiers.org/brain-bican/vocab/Donor","bican:Donor"]] = Field(["bican:Donor"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. + * In a neo4j database this MAY correspond to the neo4j label tag. + * In an RDF database it should be a biolink model class URI. +This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ... +In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") + type: Optional[List[str]] = Field(default_factory=list) + name: Optional[str] = Field(None, description="""it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + class BiologicalEntity(ThingWithTaxon, NamedThing): @@ -1948,6 +2425,7 @@ class BiologicalEntity(ThingWithTaxon, NamedThing): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/BiologicalEntity","biolink:BiologicalEntity"]] = Field(["biolink:BiologicalEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -1961,19 +2439,16 @@ class BiologicalEntity(ThingWithTaxon, NamedThing): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class GenomicEntity(ConfiguredBaseModel): has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") - class EpigenomicEntity(ConfiguredBaseModel): has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") - class BiologicalProcessOrActivity(BiologicalEntity, Occurrent, OntologyClass): """ Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system. @@ -1987,6 +2462,7 @@ class BiologicalProcessOrActivity(BiologicalEntity, Occurrent, OntologyClass): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/BiologicalProcessOrActivity","biolink:BiologicalProcessOrActivity"]] = Field(["biolink:BiologicalProcessOrActivity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -1999,7 +2475,6 @@ class BiologicalProcessOrActivity(BiologicalEntity, Occurrent, OntologyClass): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class MolecularActivity(BiologicalProcessOrActivity, Occurrent, OntologyClass): """ An execution of a molecular function carried out by a gene product or macromolecular complex. @@ -2013,6 +2488,7 @@ class MolecularActivity(BiologicalProcessOrActivity, Occurrent, OntologyClass): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MolecularActivity","biolink:MolecularActivity"]] = Field(["biolink:MolecularActivity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2025,7 +2501,6 @@ class MolecularActivity(BiologicalProcessOrActivity, Occurrent, OntologyClass): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class BiologicalProcess(BiologicalProcessOrActivity, Occurrent, OntologyClass): """ One or more causally connected executions of molecular functions @@ -2039,6 +2514,7 @@ class BiologicalProcess(BiologicalProcessOrActivity, Occurrent, OntologyClass): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/BiologicalProcess","biolink:BiologicalProcess"]] = Field(["biolink:BiologicalProcess"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2051,7 +2527,6 @@ class BiologicalProcess(BiologicalProcessOrActivity, Occurrent, OntologyClass): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class Pathway(BiologicalProcess, OntologyClass): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") @@ -2063,6 +2538,7 @@ class Pathway(BiologicalProcess, OntologyClass): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Pathway","biolink:Pathway"]] = Field(["biolink:Pathway"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2075,7 +2551,6 @@ class Pathway(BiologicalProcess, OntologyClass): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class PhysiologicalProcess(BiologicalProcess, OntologyClass): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") @@ -2087,6 +2562,7 @@ class PhysiologicalProcess(BiologicalProcess, OntologyClass): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PhysiologicalProcess","biolink:PhysiologicalProcess"]] = Field(["biolink:PhysiologicalProcess"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2099,7 +2575,6 @@ class PhysiologicalProcess(BiologicalProcess, OntologyClass): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class Behavior(BiologicalProcess, ActivityAndBehavior, OntologyClass): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") @@ -2111,6 +2586,7 @@ class Behavior(BiologicalProcess, ActivityAndBehavior, OntologyClass): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Behavior","biolink:Behavior"]] = Field(["biolink:Behavior"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2123,7 +2599,6 @@ class Behavior(BiologicalProcess, ActivityAndBehavior, OntologyClass): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class OrganismAttribute(Attribute): """ describes a characteristic of an organismal entity. @@ -2137,6 +2612,7 @@ class OrganismAttribute(Attribute): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/OrganismAttribute","biolink:OrganismAttribute"]] = Field(["biolink:OrganismAttribute"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -2147,7 +2623,6 @@ class OrganismAttribute(Attribute): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class PhenotypicQuality(OrganismAttribute): """ A property of a phenotype @@ -2161,6 +2636,7 @@ class PhenotypicQuality(OrganismAttribute): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/PhenotypicQuality","biolink:PhenotypicQuality"]] = Field(["biolink:PhenotypicQuality"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -2171,7 +2647,6 @@ class PhenotypicQuality(OrganismAttribute): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class GeneticInheritance(BiologicalEntity): """ The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc. @@ -2181,6 +2656,7 @@ class GeneticInheritance(BiologicalEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneticInheritance","biolink:GeneticInheritance"]] = Field(["biolink:GeneticInheritance"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2194,7 +2670,6 @@ class GeneticInheritance(BiologicalEntity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class OrganismalEntity(BiologicalEntity, SubjectOfInvestigation): """ A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities @@ -2204,6 +2679,7 @@ class OrganismalEntity(BiologicalEntity, SubjectOfInvestigation): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/OrganismalEntity","biolink:OrganismalEntity"]] = Field(["biolink:OrganismalEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2217,7 +2693,6 @@ class OrganismalEntity(BiologicalEntity, SubjectOfInvestigation): has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") - class Bacterium(OrganismalEntity): """ A member of a group of unicellular microorganisms lacking a nuclear membrane, that reproduce by binary fission and are often motile. @@ -2227,6 +2702,7 @@ class Bacterium(OrganismalEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Bacterium","biolink:Bacterium"]] = Field(["biolink:Bacterium"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2240,7 +2716,6 @@ class Bacterium(OrganismalEntity): has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") - class Virus(OrganismalEntity, SubjectOfInvestigation): """ A virus is a microorganism that replicates itself as a microRNA and infects the host cell. @@ -2250,6 +2725,7 @@ class Virus(OrganismalEntity, SubjectOfInvestigation): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Virus","biolink:Virus"]] = Field(["biolink:Virus"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2263,7 +2739,6 @@ class Virus(OrganismalEntity, SubjectOfInvestigation): has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") - class CellularOrganism(OrganismalEntity, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") @@ -2271,6 +2746,7 @@ class CellularOrganism(OrganismalEntity, SubjectOfInvestigation): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CellularOrganism","biolink:CellularOrganism"]] = Field(["biolink:CellularOrganism"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2284,7 +2760,6 @@ class CellularOrganism(OrganismalEntity, SubjectOfInvestigation): has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") - class Mammal(CellularOrganism, SubjectOfInvestigation): """ A member of the class Mammalia, a clade of endothermic amniotes distinguished from reptiles and birds by the possession of hair, three middle ear bones, mammary glands, and a neocortex @@ -2294,6 +2769,7 @@ class Mammal(CellularOrganism, SubjectOfInvestigation): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Mammal","biolink:Mammal"]] = Field(["biolink:Mammal"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2307,7 +2783,6 @@ class Mammal(CellularOrganism, SubjectOfInvestigation): has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") - class Human(Mammal, SubjectOfInvestigation): """ A member of the the species Homo sapiens. @@ -2317,6 +2792,7 @@ class Human(Mammal, SubjectOfInvestigation): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Human","biolink:Human"]] = Field(["biolink:Human"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2330,7 +2806,6 @@ class Human(Mammal, SubjectOfInvestigation): has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") - class Plant(CellularOrganism): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") @@ -2338,6 +2813,7 @@ class Plant(CellularOrganism): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Plant","biolink:Plant"]] = Field(["biolink:Plant"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2351,7 +2827,6 @@ class Plant(CellularOrganism): has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") - class Invertebrate(CellularOrganism): """ An animal lacking a vertebral column. This group consists of 98% of all animal species. @@ -2361,6 +2836,7 @@ class Invertebrate(CellularOrganism): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Invertebrate","biolink:Invertebrate"]] = Field(["biolink:Invertebrate"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2374,7 +2850,6 @@ class Invertebrate(CellularOrganism): has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") - class Vertebrate(CellularOrganism): """ A sub-phylum of animals consisting of those having a bony or cartilaginous vertebral column. @@ -2384,6 +2859,7 @@ class Vertebrate(CellularOrganism): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Vertebrate","biolink:Vertebrate"]] = Field(["biolink:Vertebrate"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2397,7 +2873,6 @@ class Vertebrate(CellularOrganism): has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") - class Fungus(CellularOrganism): """ A kingdom of eukaryotic, heterotrophic organisms that live as saprobes or parasites, including mushrooms, yeasts, smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi refer to those that grow as multicellular colonies (mushrooms and molds). @@ -2407,6 +2882,7 @@ class Fungus(CellularOrganism): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Fungus","biolink:Fungus"]] = Field(["biolink:Fungus"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2420,7 +2896,6 @@ class Fungus(CellularOrganism): has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") - class LifeStage(OrganismalEntity): """ A stage of development or growth of an organism, including post-natal adult stages @@ -2430,6 +2905,7 @@ class LifeStage(OrganismalEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/LifeStage","biolink:LifeStage"]] = Field(["biolink:LifeStage"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2443,7 +2919,6 @@ class LifeStage(OrganismalEntity): has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") - class IndividualOrganism(OrganismalEntity, SubjectOfInvestigation): """ An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576 @@ -2453,6 +2928,7 @@ class IndividualOrganism(OrganismalEntity, SubjectOfInvestigation): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/IndividualOrganism","biolink:IndividualOrganism"]] = Field(["biolink:IndividualOrganism"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2466,7 +2942,6 @@ class IndividualOrganism(OrganismalEntity, SubjectOfInvestigation): has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") - class PopulationOfIndividualOrganisms(OrganismalEntity, SubjectOfInvestigation): """ A collection of individuals from the same taxonomic class distinguished by one or more characteristics. Characteristics can include, but are not limited to, shared geographic location, genetics, phenotypes. @@ -2476,6 +2951,7 @@ class PopulationOfIndividualOrganisms(OrganismalEntity, SubjectOfInvestigation): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PopulationOfIndividualOrganisms","biolink:PopulationOfIndividualOrganisms"]] = Field(["biolink:PopulationOfIndividualOrganisms"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2489,7 +2965,6 @@ class PopulationOfIndividualOrganisms(OrganismalEntity, SubjectOfInvestigation): has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") - class StudyPopulation(PopulationOfIndividualOrganisms): """ A group of people banded together or treated as a group as participants in a research study. @@ -2499,6 +2974,7 @@ class StudyPopulation(PopulationOfIndividualOrganisms): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/StudyPopulation","biolink:StudyPopulation"]] = Field(["biolink:StudyPopulation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2512,7 +2988,6 @@ class StudyPopulation(PopulationOfIndividualOrganisms): has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") - class DiseaseOrPhenotypicFeature(BiologicalEntity): """ Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate. Please see definitions of phenotypic feature and disease in this model for their independent descriptions. This class is helpful to enforce domains and ranges that may involve either a disease or a phenotypic feature. @@ -2522,6 +2997,7 @@ class DiseaseOrPhenotypicFeature(BiologicalEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DiseaseOrPhenotypicFeature","biolink:DiseaseOrPhenotypicFeature"]] = Field(["biolink:DiseaseOrPhenotypicFeature"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2535,7 +3011,6 @@ class DiseaseOrPhenotypicFeature(BiologicalEntity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class Disease(DiseaseOrPhenotypicFeature): """ A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. @@ -2545,6 +3020,7 @@ class Disease(DiseaseOrPhenotypicFeature): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Disease","biolink:Disease"]] = Field(["biolink:Disease"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2558,7 +3034,6 @@ class Disease(DiseaseOrPhenotypicFeature): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class PhenotypicFeature(DiseaseOrPhenotypicFeature): """ A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment. @@ -2568,6 +3043,7 @@ class PhenotypicFeature(DiseaseOrPhenotypicFeature): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PhenotypicFeature","biolink:PhenotypicFeature"]] = Field(["biolink:PhenotypicFeature"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2581,7 +3057,6 @@ class PhenotypicFeature(DiseaseOrPhenotypicFeature): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class BehavioralFeature(PhenotypicFeature): """ A phenotypic feature which is behavioral in nature. @@ -2591,6 +3066,7 @@ class BehavioralFeature(PhenotypicFeature): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/BehavioralFeature","biolink:BehavioralFeature"]] = Field(["biolink:BehavioralFeature"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2604,7 +3080,6 @@ class BehavioralFeature(PhenotypicFeature): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class AnatomicalEntity(OrganismalEntity, PhysicalEssence): """ A subcellular location, cell type or gross anatomical part @@ -2614,6 +3089,7 @@ class AnatomicalEntity(OrganismalEntity, PhysicalEssence): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/AnatomicalEntity","biolink:AnatomicalEntity"]] = Field(["biolink:AnatomicalEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2627,7 +3103,6 @@ class AnatomicalEntity(OrganismalEntity, PhysicalEssence): has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") - class CellularComponent(AnatomicalEntity): """ A location in or around a cell @@ -2637,6 +3112,7 @@ class CellularComponent(AnatomicalEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CellularComponent","biolink:CellularComponent"]] = Field(["biolink:CellularComponent"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2650,7 +3126,6 @@ class CellularComponent(AnatomicalEntity): has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") - class Cell(AnatomicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") @@ -2658,6 +3133,7 @@ class Cell(AnatomicalEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Cell","biolink:Cell"]] = Field(["biolink:Cell"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2671,7 +3147,6 @@ class Cell(AnatomicalEntity): has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") - class CellLine(OrganismalEntity, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") @@ -2679,6 +3154,7 @@ class CellLine(OrganismalEntity, SubjectOfInvestigation): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CellLine","biolink:CellLine"]] = Field(["biolink:CellLine"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2692,7 +3168,6 @@ class CellLine(OrganismalEntity, SubjectOfInvestigation): has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") - class GrossAnatomicalStructure(AnatomicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") @@ -2700,6 +3175,7 @@ class GrossAnatomicalStructure(AnatomicalEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GrossAnatomicalStructure","biolink:GrossAnatomicalStructure"]] = Field(["biolink:GrossAnatomicalStructure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2713,7 +3189,6 @@ class GrossAnatomicalStructure(AnatomicalEntity): has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") - class ChemicalEntityOrGeneOrGeneProduct(ConfiguredBaseModel): """ A union of chemical entities and children, and gene or gene product. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities. @@ -2721,7 +3196,6 @@ class ChemicalEntityOrGeneOrGeneProduct(ConfiguredBaseModel): None - class RegulatoryRegion(ChemicalEntityOrGeneOrGeneProduct, GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass): """ A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- to affect the transcription of gene @@ -2733,6 +3207,7 @@ class RegulatoryRegion(ChemicalEntityOrGeneOrGeneProduct, GenomicEntity, Biologi provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/RegulatoryRegion","biolink:RegulatoryRegion"]] = Field(["biolink:RegulatoryRegion"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2745,7 +3220,6 @@ class RegulatoryRegion(ChemicalEntityOrGeneOrGeneProduct, GenomicEntity, Biologi has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class AccessibleDnaRegion(RegulatoryRegion, ChemicalEntityOrGeneOrGeneProduct, GenomicEntity, PhysicalEssence, OntologyClass): """ A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as DNase-I or Tn5 Transpose @@ -2757,6 +3231,7 @@ class AccessibleDnaRegion(RegulatoryRegion, ChemicalEntityOrGeneOrGeneProduct, G provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/AccessibleDnaRegion","biolink:AccessibleDnaRegion"]] = Field(["biolink:AccessibleDnaRegion"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2769,7 +3244,6 @@ class AccessibleDnaRegion(RegulatoryRegion, ChemicalEntityOrGeneOrGeneProduct, G has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class TranscriptionFactorBindingSite(RegulatoryRegion, ChemicalEntityOrGeneOrGeneProduct, GenomicEntity, PhysicalEssence, OntologyClass): """ A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that modulates gene transcription @@ -2781,6 +3255,7 @@ class TranscriptionFactorBindingSite(RegulatoryRegion, ChemicalEntityOrGeneOrGen provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/TranscriptionFactorBindingSite","biolink:TranscriptionFactorBindingSite"]] = Field(["biolink:TranscriptionFactorBindingSite"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2793,7 +3268,6 @@ class TranscriptionFactorBindingSite(RegulatoryRegion, ChemicalEntityOrGeneOrGen has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ChemicalEntityOrProteinOrPolypeptide(ConfiguredBaseModel): """ A union of chemical entities and children, and protein and polypeptide. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities. @@ -2801,7 +3275,6 @@ class ChemicalEntityOrProteinOrPolypeptide(ConfiguredBaseModel): None - class ChemicalEntity(ChemicalEntityOrProteinOrPolypeptide, ChemicalEntityOrGeneOrGeneProduct, PhysicalEssence, NamedThing, ChemicalOrDrugOrTreatment): """ A chemical entity is a physical entity that pertains to chemistry or biochemistry. @@ -2814,6 +3287,7 @@ class ChemicalEntity(ChemicalEntityOrProteinOrPolypeptide, ChemicalEntityOrGeneO provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalEntity","biolink:ChemicalEntity"]] = Field(["biolink:ChemicalEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2827,7 +3301,6 @@ class ChemicalEntity(ChemicalEntityOrProteinOrPolypeptide, ChemicalEntityOrGeneO has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class MolecularEntity(ChemicalEntity): """ A molecular entity is a chemical entity composed of individual or covalently bonded atoms. @@ -2841,6 +3314,7 @@ class MolecularEntity(ChemicalEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MolecularEntity","biolink:MolecularEntity"]] = Field(["biolink:MolecularEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2854,7 +3328,6 @@ class MolecularEntity(ChemicalEntity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class SmallMolecule(MolecularEntity): """ A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion). @@ -2868,6 +3341,7 @@ class SmallMolecule(MolecularEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/SmallMolecule","biolink:SmallMolecule"]] = Field(["biolink:SmallMolecule"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2881,7 +3355,6 @@ class SmallMolecule(MolecularEntity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ChemicalMixture(ChemicalEntity): """ A chemical mixture is a chemical entity composed of two or more molecular entities. @@ -2898,6 +3371,7 @@ class ChemicalMixture(ChemicalEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalMixture","biolink:ChemicalMixture"]] = Field(["biolink:ChemicalMixture"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2911,7 +3385,6 @@ class ChemicalMixture(ChemicalEntity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class NucleicAcidEntity(MolecularEntity, GenomicEntity, ThingWithTaxon, PhysicalEssence, OntologyClass): """ A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included. @@ -2929,6 +3402,7 @@ class NucleicAcidEntity(MolecularEntity, GenomicEntity, ThingWithTaxon, Physical provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/NucleicAcidEntity","biolink:NucleicAcidEntity"]] = Field(["biolink:NucleicAcidEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -2941,7 +3415,6 @@ class NucleicAcidEntity(MolecularEntity, GenomicEntity, ThingWithTaxon, Physical has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class MolecularMixture(ChemicalMixture): """ A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry. @@ -2958,6 +3431,7 @@ class MolecularMixture(ChemicalMixture): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MolecularMixture","biolink:MolecularMixture"]] = Field(["biolink:MolecularMixture"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -2971,7 +3445,6 @@ class MolecularMixture(ChemicalMixture): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ComplexMolecularMixture(ChemicalMixture): """ A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry. @@ -2988,6 +3461,7 @@ class ComplexMolecularMixture(ChemicalMixture): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ComplexMolecularMixture","biolink:ComplexMolecularMixture"]] = Field(["biolink:ComplexMolecularMixture"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -3001,7 +3475,6 @@ class ComplexMolecularMixture(ChemicalMixture): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ProcessedMaterial(ChemicalMixture): """ A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during material processing. @@ -3018,6 +3491,7 @@ class ProcessedMaterial(ChemicalMixture): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ProcessedMaterial","biolink:ProcessedMaterial"]] = Field(["biolink:ProcessedMaterial"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -3031,7 +3505,6 @@ class ProcessedMaterial(ChemicalMixture): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class Drug(MolecularMixture, ChemicalOrDrugOrTreatment, OntologyClass): """ A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease @@ -3049,6 +3522,7 @@ class Drug(MolecularMixture, ChemicalOrDrugOrTreatment, OntologyClass): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Drug","biolink:Drug"]] = Field(["biolink:Drug"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -3061,7 +3535,6 @@ class Drug(MolecularMixture, ChemicalOrDrugOrTreatment, OntologyClass): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class EnvironmentalFoodContaminant(ChemicalEntity): trade_name: Optional[str] = Field(None) @@ -3072,6 +3545,7 @@ class EnvironmentalFoodContaminant(ChemicalEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/EnvironmentalFoodContaminant","biolink:EnvironmentalFoodContaminant"]] = Field(["biolink:EnvironmentalFoodContaminant"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -3085,7 +3559,6 @@ class EnvironmentalFoodContaminant(ChemicalEntity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class FoodAdditive(ChemicalEntity): trade_name: Optional[str] = Field(None) @@ -3096,6 +3569,7 @@ class FoodAdditive(ChemicalEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/FoodAdditive","biolink:FoodAdditive"]] = Field(["biolink:FoodAdditive"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -3109,7 +3583,6 @@ class FoodAdditive(ChemicalEntity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class Food(ChemicalMixture): """ A substance consumed by a living organism as a source of nutrition @@ -3126,6 +3599,7 @@ class Food(ChemicalMixture): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Food","biolink:Food"]] = Field(["biolink:Food"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -3139,7 +3613,6 @@ class Food(ChemicalMixture): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class MacromolecularMachineMixin(ConfiguredBaseModel): """ A union of gene locus, gene product, and macromolecular complex. These are the basic units of function in a cell. They either carry out individual biological activities, or they encode molecules which do this. @@ -3147,7 +3620,6 @@ class MacromolecularMachineMixin(ConfiguredBaseModel): name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") - class GeneOrGeneProduct(MacromolecularMachineMixin): """ A union of gene loci or gene products. Frequently an identifier for one will be used as proxy for another @@ -3155,13 +3627,11 @@ class GeneOrGeneProduct(MacromolecularMachineMixin): name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") - class Gene(GeneOrGeneProduct, ChemicalEntityOrGeneOrGeneProduct, GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass): """ A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions. """ symbol: Optional[str] = Field(None, description="""Symbol for a particular thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") @@ -3169,6 +3639,7 @@ class Gene(GeneOrGeneProduct, ChemicalEntityOrGeneOrGeneProduct, GenomicEntity, in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Gene","biolink:Gene"]] = Field(["biolink:Gene"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -3181,7 +3652,6 @@ class Gene(GeneOrGeneProduct, ChemicalEntityOrGeneOrGeneProduct, GenomicEntity, has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class GeneAnnotation(Gene): """ An annotation describing the location, boundaries, and functions of individual genes within a genome annotation. @@ -3190,7 +3660,6 @@ class GeneAnnotation(Gene): molecular_type: Optional[BioType] = Field(None) source_id: Optional[str] = Field(None, description="""The authority specific identifier.""") symbol: Optional[str] = Field(None, description="""Symbol for a particular thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") @@ -3198,6 +3667,7 @@ class GeneAnnotation(Gene): in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://identifiers.org/brain-bican/vocab/GeneAnnotation","bican:GeneAnnotation"]] = Field(["bican:GeneAnnotation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -3210,7 +3680,6 @@ class GeneAnnotation(Gene): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class GeneProductMixin(GeneOrGeneProduct): """ The functional molecular product of a single gene locus. Gene products are either proteins or functional RNA molecules. @@ -3220,7 +3689,6 @@ class GeneProductMixin(GeneOrGeneProduct): name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") - class GeneProductIsoformMixin(GeneProductMixin): """ This is an abstract class that can be mixed in with different kinds of gene products to indicate that the gene product is intended to represent a specific isoform rather than a canonical or reference or generic product. The designation of canonical or reference may be arbitrary, or it may represent the superclass of all isoforms. @@ -3230,7 +3698,6 @@ class GeneProductIsoformMixin(GeneProductMixin): name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") - class MacromolecularComplex(MacromolecularMachineMixin, BiologicalEntity): """ A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. @@ -3241,6 +3708,7 @@ class MacromolecularComplex(MacromolecularMachineMixin, BiologicalEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MacromolecularComplex","biolink:MacromolecularComplex"]] = Field(["biolink:MacromolecularComplex"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -3253,7 +3721,6 @@ class MacromolecularComplex(MacromolecularMachineMixin, BiologicalEntity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class NucleosomeModification(GeneProductIsoformMixin, EpigenomicEntity, GenomicEntity, BiologicalEntity): """ A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A. @@ -3264,6 +3731,7 @@ class NucleosomeModification(GeneProductIsoformMixin, EpigenomicEntity, GenomicE provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/NucleosomeModification","biolink:NucleosomeModification"]] = Field(["biolink:NucleosomeModification"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -3275,10 +3743,8 @@ class NucleosomeModification(GeneProductIsoformMixin, EpigenomicEntity, GenomicE name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") - class Genome(GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass): """ A genome is the sum of genetic material within a cell or virion. @@ -3290,6 +3756,7 @@ class Genome(GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Genome","biolink:Genome"]] = Field(["biolink:Genome"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -3302,15 +3769,15 @@ class Genome(GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class GenomeAnnotation(Genome): """ Location and nomenclature of genes and all of the coding regions in a genome assembly and the classification of genes and transcripts into types. """ reference_assembly: Optional[str] = Field(None) version: Optional[str] = Field(None) - digest: List[str] = Field(default_factory=list) + digest: List[str] = Field(default_factory=list, description="""Stores checksum information.""") content_url: Optional[List[str]] = Field(default_factory=list) + authority: Optional[str] = Field(None, description="""The organization responsible for publishing the data.""") has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") @@ -3318,6 +3785,7 @@ class GenomeAnnotation(Genome): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://identifiers.org/brain-bican/vocab/GenomeAnnotation","bican:GenomeAnnotation"]] = Field(["bican:GenomeAnnotation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -3330,7 +3798,6 @@ class GenomeAnnotation(Genome): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class Exon(NucleicAcidEntity): """ A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing. @@ -3348,6 +3815,7 @@ class Exon(NucleicAcidEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Exon","biolink:Exon"]] = Field(["biolink:Exon"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -3360,7 +3828,6 @@ class Exon(NucleicAcidEntity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class Transcript(NucleicAcidEntity): """ An RNA synthesized on a DNA or RNA template by an RNA polymerase. @@ -3378,6 +3845,7 @@ class Transcript(NucleicAcidEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Transcript","biolink:Transcript"]] = Field(["biolink:Transcript"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -3390,7 +3858,6 @@ class Transcript(NucleicAcidEntity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class CodingSequence(NucleicAcidEntity): has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") @@ -3406,6 +3873,7 @@ class CodingSequence(NucleicAcidEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CodingSequence","biolink:CodingSequence"]] = Field(["biolink:CodingSequence"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -3418,7 +3886,6 @@ class CodingSequence(NucleicAcidEntity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class Polypeptide(ChemicalEntityOrProteinOrPolypeptide, ChemicalEntityOrGeneOrGeneProduct, BiologicalEntity): """ A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule. @@ -3428,6 +3895,7 @@ class Polypeptide(ChemicalEntityOrProteinOrPolypeptide, ChemicalEntityOrGeneOrGe provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Polypeptide","biolink:Polypeptide"]] = Field(["biolink:Polypeptide"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -3441,7 +3909,6 @@ class Polypeptide(ChemicalEntityOrProteinOrPolypeptide, ChemicalEntityOrGeneOrGe has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class Protein(Polypeptide, GeneProductMixin): """ A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA @@ -3465,7 +3932,6 @@ class Protein(Polypeptide, GeneProductMixin): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ProteinIsoform(Protein, GeneProductIsoformMixin): """ Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/ @@ -3489,7 +3955,6 @@ class ProteinIsoform(Protein, GeneProductIsoformMixin): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class PosttranslationalModification(GeneProductIsoformMixin, BiologicalEntity): """ A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, protein ubiquitination. @@ -3499,6 +3964,7 @@ class PosttranslationalModification(GeneProductIsoformMixin, BiologicalEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PosttranslationalModification","biolink:PosttranslationalModification"]] = Field(["biolink:PosttranslationalModification"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -3510,10 +3976,8 @@ class PosttranslationalModification(GeneProductIsoformMixin, BiologicalEntity): name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") - class NucleicAcidSequenceMotif(BiologicalEntity): """ A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, transcription factor binding consensus sequences. @@ -3523,6 +3987,7 @@ class NucleicAcidSequenceMotif(BiologicalEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/NucleicAcidSequenceMotif","biolink:NucleicAcidSequenceMotif"]] = Field(["biolink:NucleicAcidSequenceMotif"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -3536,7 +4001,6 @@ class NucleicAcidSequenceMotif(BiologicalEntity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class RNAProduct(Transcript, GeneProductMixin): synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") @@ -3565,7 +4029,6 @@ class RNAProduct(Transcript, GeneProductMixin): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class RNAProductIsoform(RNAProduct, GeneProductIsoformMixin): """ Represents a protein that is a specific isoform of the canonical or reference RNA @@ -3596,7 +4059,6 @@ class RNAProductIsoform(RNAProduct, GeneProductIsoformMixin): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class NoncodingRNAProduct(RNAProduct): synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") @@ -3625,7 +4087,6 @@ class NoncodingRNAProduct(RNAProduct): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class MicroRNA(NoncodingRNAProduct): synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") @@ -3654,7 +4115,6 @@ class MicroRNA(NoncodingRNAProduct): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class SiRNA(NoncodingRNAProduct): """ A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules. @@ -3685,7 +4145,6 @@ class SiRNA(NoncodingRNAProduct): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class GeneGroupingMixin(ConfiguredBaseModel): """ any grouping of multiple genes or gene products @@ -3693,7 +4152,6 @@ class GeneGroupingMixin(ConfiguredBaseModel): has_gene_or_gene_product: Optional[List[str]] = Field(None, description="""connects an entity with one or more gene or gene products""") - class ProteinDomain(GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProduct, BiologicalEntity): """ A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain. @@ -3704,6 +4162,7 @@ class ProteinDomain(GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProduct, Biolog provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ProteinDomain","biolink:ProteinDomain"]] = Field(["biolink:ProteinDomain"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -3717,7 +4176,6 @@ class ProteinDomain(GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProduct, Biolog has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ProteinFamily(GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProduct, BiologicalEntity): has_gene_or_gene_product: Optional[List[str]] = Field(None, description="""connects an entity with one or more gene or gene products""") @@ -3726,6 +4184,7 @@ class ProteinFamily(GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProduct, Biolog provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ProteinFamily","biolink:ProteinFamily"]] = Field(["biolink:ProteinFamily"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -3739,7 +4198,6 @@ class ProteinFamily(GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProduct, Biolog has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class GeneFamily(GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProduct, BiologicalEntity): """ any grouping of multiple genes or gene products related by common descent @@ -3750,6 +4208,7 @@ class GeneFamily(GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProduct, Biologica provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneFamily","biolink:GeneFamily"]] = Field(["biolink:GeneFamily"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -3763,7 +4222,6 @@ class GeneFamily(GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProduct, Biologica has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class Zygosity(Attribute): name: Optional[str] = Field(None, description="""The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.""") @@ -3775,6 +4233,7 @@ class Zygosity(Attribute): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/Zygosity","biolink:Zygosity"]] = Field(["biolink:Zygosity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -3785,7 +4244,6 @@ class Zygosity(Attribute): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class Genotype(GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass): """ An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background @@ -3798,6 +4256,7 @@ class Genotype(GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Genotype","biolink:Genotype"]] = Field(["biolink:Genotype"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -3810,7 +4269,6 @@ class Genotype(GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class Haplotype(GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass): """ A set of zero or more Alleles on a single instance of a Sequence[VMC] @@ -3822,6 +4280,7 @@ class Haplotype(GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass) provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Haplotype","biolink:Haplotype"]] = Field(["biolink:Haplotype"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -3834,7 +4293,6 @@ class Haplotype(GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass) has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class SequenceVariant(GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass): """ A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. @@ -3847,6 +4305,7 @@ class SequenceVariant(GenomicEntity, BiologicalEntity, PhysicalEssence, Ontology provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/SequenceVariant","biolink:SequenceVariant"]] = Field(["biolink:SequenceVariant"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -3859,7 +4318,6 @@ class SequenceVariant(GenomicEntity, BiologicalEntity, PhysicalEssence, Ontology has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class Snv(SequenceVariant): """ SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist @@ -3872,6 +4330,7 @@ class Snv(SequenceVariant): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Snv","biolink:Snv"]] = Field(["biolink:Snv"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -3884,7 +4343,6 @@ class Snv(SequenceVariant): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ReagentTargetedGene(GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass): """ A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi. @@ -3896,6 +4354,7 @@ class ReagentTargetedGene(GenomicEntity, BiologicalEntity, PhysicalEssence, Onto provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ReagentTargetedGene","biolink:ReagentTargetedGene"]] = Field(["biolink:ReagentTargetedGene"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -3908,7 +4367,6 @@ class ReagentTargetedGene(GenomicEntity, BiologicalEntity, PhysicalEssence, Onto has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ClinicalAttribute(Attribute): """ Attributes relating to a clinical manifestation @@ -3922,6 +4380,7 @@ class ClinicalAttribute(Attribute): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalAttribute","biolink:ClinicalAttribute"]] = Field(["biolink:ClinicalAttribute"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -3932,7 +4391,6 @@ class ClinicalAttribute(Attribute): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ClinicalMeasurement(ClinicalAttribute): """ A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot. @@ -3946,6 +4404,7 @@ class ClinicalMeasurement(ClinicalAttribute): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalMeasurement","biolink:ClinicalMeasurement"]] = Field(["biolink:ClinicalMeasurement"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -3956,7 +4415,6 @@ class ClinicalMeasurement(ClinicalAttribute): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ClinicalModifier(ClinicalAttribute): """ Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects @@ -3970,6 +4428,7 @@ class ClinicalModifier(ClinicalAttribute): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalModifier","biolink:ClinicalModifier"]] = Field(["biolink:ClinicalModifier"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -3980,7 +4439,6 @@ class ClinicalModifier(ClinicalAttribute): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ClinicalCourse(ClinicalAttribute): """ The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual @@ -3994,6 +4452,7 @@ class ClinicalCourse(ClinicalAttribute): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalCourse","biolink:ClinicalCourse"]] = Field(["biolink:ClinicalCourse"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4004,7 +4463,6 @@ class ClinicalCourse(ClinicalAttribute): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class Onset(ClinicalCourse): """ The age group in which (disease) symptom manifestations appear @@ -4018,6 +4476,7 @@ class Onset(ClinicalCourse): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/Onset","biolink:Onset"]] = Field(["biolink:Onset"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4028,7 +4487,6 @@ class Onset(ClinicalCourse): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ClinicalEntity(NamedThing): """ Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities @@ -4036,6 +4494,7 @@ class ClinicalEntity(NamedThing): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalEntity","biolink:ClinicalEntity"]] = Field(["biolink:ClinicalEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4049,12 +4508,12 @@ class ClinicalEntity(NamedThing): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ClinicalTrial(ClinicalEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalTrial","biolink:ClinicalTrial"]] = Field(["biolink:ClinicalTrial"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4068,12 +4527,12 @@ class ClinicalTrial(ClinicalEntity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ClinicalIntervention(ClinicalEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalIntervention","biolink:ClinicalIntervention"]] = Field(["biolink:ClinicalIntervention"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4087,7 +4546,6 @@ class ClinicalIntervention(ClinicalEntity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ClinicalFinding(PhenotypicFeature): """ this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some statistical score, for example, a p value in genetic associations. @@ -4097,6 +4555,7 @@ class ClinicalFinding(PhenotypicFeature): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalFinding","biolink:ClinicalFinding"]] = Field(["biolink:ClinicalFinding"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4110,12 +4569,12 @@ class ClinicalFinding(PhenotypicFeature): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class Hospitalization(ClinicalIntervention): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Hospitalization","biolink:Hospitalization"]] = Field(["biolink:Hospitalization"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4129,7 +4588,6 @@ class Hospitalization(ClinicalIntervention): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class SocioeconomicAttribute(Attribute): """ Attributes relating to a socioeconomic manifestation @@ -4143,6 +4601,7 @@ class SocioeconomicAttribute(Attribute): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/SocioeconomicAttribute","biolink:SocioeconomicAttribute"]] = Field(["biolink:SocioeconomicAttribute"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4153,7 +4612,6 @@ class SocioeconomicAttribute(Attribute): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class Case(IndividualOrganism, SubjectOfInvestigation): """ An individual (human) organism that has a patient role in some clinical context. @@ -4163,6 +4621,7 @@ class Case(IndividualOrganism, SubjectOfInvestigation): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Case","biolink:Case"]] = Field(["biolink:Case"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4176,7 +4635,6 @@ class Case(IndividualOrganism, SubjectOfInvestigation): has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") - class Cohort(StudyPopulation, SubjectOfInvestigation): """ A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that samples a cohort, performing a cross-section at intervals through time. @@ -4186,6 +4644,7 @@ class Cohort(StudyPopulation, SubjectOfInvestigation): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Cohort","biolink:Cohort"]] = Field(["biolink:Cohort"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4199,7 +4658,6 @@ class Cohort(StudyPopulation, SubjectOfInvestigation): has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") - class ExposureEvent(OntologyClass): """ A (possibly time bounded) incidence of a feature of the environment of an organism that influences one or more phenotypic features of that organism, potentially mediated by genes @@ -4208,7 +4666,6 @@ class ExposureEvent(OntologyClass): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") - class GenomicBackgroundExposure(ExposureEvent, GeneGroupingMixin, GenomicEntity, ThingWithTaxon, PhysicalEssence, Attribute, OntologyClass): """ A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome. @@ -4227,6 +4684,7 @@ class GenomicBackgroundExposure(ExposureEvent, GeneGroupingMixin, GenomicEntity, provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/GenomicBackgroundExposure","biolink:GenomicBackgroundExposure"]] = Field(["biolink:GenomicBackgroundExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4237,7 +4695,6 @@ class GenomicBackgroundExposure(ExposureEvent, GeneGroupingMixin, GenomicEntity, has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class PathologicalEntityMixin(ConfiguredBaseModel): """ A pathological (abnormal) structure or process. @@ -4245,7 +4702,6 @@ class PathologicalEntityMixin(ConfiguredBaseModel): None - class PathologicalProcess(PathologicalEntityMixin, BiologicalProcess): """ A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level. @@ -4259,6 +4715,7 @@ class PathologicalProcess(PathologicalEntityMixin, BiologicalProcess): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PathologicalProcess","biolink:PathologicalProcess"]] = Field(["biolink:PathologicalProcess"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. @@ -4271,7 +4728,6 @@ class PathologicalProcess(PathologicalEntityMixin, BiologicalProcess): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class PathologicalProcessExposure(ExposureEvent, Attribute): """ A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease. @@ -4286,6 +4742,7 @@ class PathologicalProcessExposure(ExposureEvent, Attribute): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/PathologicalProcessExposure","biolink:PathologicalProcessExposure"]] = Field(["biolink:PathologicalProcessExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4296,7 +4753,6 @@ class PathologicalProcessExposure(ExposureEvent, Attribute): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class PathologicalAnatomicalStructure(PathologicalEntityMixin, AnatomicalEntity): """ An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level. @@ -4306,6 +4762,7 @@ class PathologicalAnatomicalStructure(PathologicalEntityMixin, AnatomicalEntity) provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PathologicalAnatomicalStructure","biolink:PathologicalAnatomicalStructure"]] = Field(["biolink:PathologicalAnatomicalStructure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4319,7 +4776,6 @@ class PathologicalAnatomicalStructure(PathologicalEntityMixin, AnatomicalEntity) has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") - class PathologicalAnatomicalExposure(ExposureEvent, Attribute): """ An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to an ischemic disease outcome. @@ -4334,6 +4790,7 @@ class PathologicalAnatomicalExposure(ExposureEvent, Attribute): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/PathologicalAnatomicalExposure","biolink:PathologicalAnatomicalExposure"]] = Field(["biolink:PathologicalAnatomicalExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4344,7 +4801,6 @@ class PathologicalAnatomicalExposure(ExposureEvent, Attribute): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class DiseaseOrPhenotypicFeatureExposure(PathologicalEntityMixin, ExposureEvent, Attribute): """ A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer. @@ -4359,6 +4815,7 @@ class DiseaseOrPhenotypicFeatureExposure(PathologicalEntityMixin, ExposureEvent, provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/DiseaseOrPhenotypicFeatureExposure","biolink:DiseaseOrPhenotypicFeatureExposure"]] = Field(["biolink:DiseaseOrPhenotypicFeatureExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4369,7 +4826,6 @@ class DiseaseOrPhenotypicFeatureExposure(PathologicalEntityMixin, ExposureEvent, has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ChemicalExposure(ExposureEvent, Attribute): """ A chemical exposure is an intake of a particular chemical entity. @@ -4384,6 +4840,7 @@ class ChemicalExposure(ExposureEvent, Attribute): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalExposure","biolink:ChemicalExposure"]] = Field(["biolink:ChemicalExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4394,7 +4851,6 @@ class ChemicalExposure(ExposureEvent, Attribute): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ComplexChemicalExposure(Attribute): """ A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug. @@ -4408,6 +4864,7 @@ class ComplexChemicalExposure(Attribute): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/ComplexChemicalExposure","biolink:ComplexChemicalExposure"]] = Field(["biolink:ComplexChemicalExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4418,7 +4875,6 @@ class ComplexChemicalExposure(Attribute): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class DrugExposure(ChemicalExposure, ExposureEvent): """ A drug exposure is an intake of a particular drug. @@ -4433,6 +4889,7 @@ class DrugExposure(ChemicalExposure, ExposureEvent): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/DrugExposure","biolink:DrugExposure"]] = Field(["biolink:DrugExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4443,7 +4900,6 @@ class DrugExposure(ChemicalExposure, ExposureEvent): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class DrugToGeneInteractionExposure(DrugExposure, GeneGroupingMixin): """ drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are known to constitute an 'exposure' to the organism, leading to or influencing an outcome. @@ -4459,6 +4915,7 @@ class DrugToGeneInteractionExposure(DrugExposure, GeneGroupingMixin): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/DrugToGeneInteractionExposure","biolink:DrugToGeneInteractionExposure"]] = Field(["biolink:DrugToGeneInteractionExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4469,7 +4926,6 @@ class DrugToGeneInteractionExposure(DrugExposure, GeneGroupingMixin): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class Treatment(ExposureEvent, NamedThing, ChemicalOrDrugOrTreatment): """ A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures @@ -4481,6 +4937,7 @@ class Treatment(ExposureEvent, NamedThing, ChemicalOrDrugOrTreatment): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Treatment","biolink:Treatment"]] = Field(["biolink:Treatment"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. @@ -4494,7 +4951,6 @@ class Treatment(ExposureEvent, NamedThing, ChemicalOrDrugOrTreatment): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class BioticExposure(ExposureEvent, Attribute): """ An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses). @@ -4509,6 +4965,7 @@ class BioticExposure(ExposureEvent, Attribute): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/BioticExposure","biolink:BioticExposure"]] = Field(["biolink:BioticExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4519,7 +4976,6 @@ class BioticExposure(ExposureEvent, Attribute): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class EnvironmentalExposure(ExposureEvent, Attribute): """ A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), atmospheric (heat, cold, general pollution) and water-born contaminants. @@ -4534,6 +4990,7 @@ class EnvironmentalExposure(ExposureEvent, Attribute): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/EnvironmentalExposure","biolink:EnvironmentalExposure"]] = Field(["biolink:EnvironmentalExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4544,7 +5001,6 @@ class EnvironmentalExposure(ExposureEvent, Attribute): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class GeographicExposure(EnvironmentalExposure, ExposureEvent): """ A geographic exposure is a factor relating to geographic proximity to some impactful entity. @@ -4559,6 +5015,7 @@ class GeographicExposure(EnvironmentalExposure, ExposureEvent): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/GeographicExposure","biolink:GeographicExposure"]] = Field(["biolink:GeographicExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4569,7 +5026,6 @@ class GeographicExposure(EnvironmentalExposure, ExposureEvent): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class BehavioralExposure(ExposureEvent, Attribute): """ A behavioral exposure is a factor relating to behavior impacting an individual. @@ -4584,6 +5040,7 @@ class BehavioralExposure(ExposureEvent, Attribute): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/BehavioralExposure","biolink:BehavioralExposure"]] = Field(["biolink:BehavioralExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4594,7 +5051,6 @@ class BehavioralExposure(ExposureEvent, Attribute): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class SocioeconomicExposure(ExposureEvent, Attribute): """ A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty). @@ -4609,6 +5065,7 @@ class SocioeconomicExposure(ExposureEvent, Attribute): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") + synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/SocioeconomicExposure","biolink:SocioeconomicExposure"]] = Field(["biolink:SocioeconomicExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. * In a neo4j database this MAY correspond to the neo4j label tag. * In an RDF database it should be a biolink model class URI. @@ -4619,7 +5076,6 @@ class SocioeconomicExposure(ExposureEvent, Attribute): has_attribute: List[str] = Field(..., description="""connects any entity to an attribute""") - class Outcome(ConfiguredBaseModel): """ An entity that has the role of being the consequence of an exposure event. This is an abstract mixin grouping of various categories of possible biological or non-biological (e.g. clinical) outcomes. @@ -4627,7 +5083,6 @@ class Outcome(ConfiguredBaseModel): None - class PathologicalProcessOutcome(Outcome): """ An outcome resulting from an exposure event which is the manifestation of a pathological process. @@ -4635,7 +5090,6 @@ class PathologicalProcessOutcome(Outcome): None - class PathologicalAnatomicalOutcome(Outcome): """ An outcome resulting from an exposure event which is the manifestation of an abnormal anatomical structure. @@ -4643,7 +5097,6 @@ class PathologicalAnatomicalOutcome(Outcome): None - class DiseaseOrPhenotypicFeatureOutcome(Outcome): """ Physiological outcomes resulting from an exposure event which is the manifestation of a disease or other characteristic phenotype. @@ -4651,7 +5104,6 @@ class DiseaseOrPhenotypicFeatureOutcome(Outcome): None - class BehavioralOutcome(Outcome): """ An outcome resulting from an exposure event which is the manifestation of human behavior. @@ -4659,7 +5111,6 @@ class BehavioralOutcome(Outcome): None - class HospitalizationOutcome(Outcome): """ An outcome resulting from an exposure event which is the increased manifestation of acute (e.g. emergency room visit) or chronic (inpatient) hospitalization. @@ -4667,7 +5118,6 @@ class HospitalizationOutcome(Outcome): None - class MortalityOutcome(Outcome): """ An outcome of death from resulting from an exposure event. @@ -4675,7 +5125,6 @@ class MortalityOutcome(Outcome): None - class EpidemiologicalOutcome(Outcome): """ An epidemiological outcome, such as societal disease burden, resulting from an exposure event. @@ -4683,7 +5132,6 @@ class EpidemiologicalOutcome(Outcome): None - class SocioeconomicOutcome(Outcome): """ An general social or economic outcome, such as healthcare costs, utilization, etc., resulting from an exposure event @@ -4691,7 +5139,6 @@ class SocioeconomicOutcome(Outcome): None - class Association(Entity): """ A typed association between two entities, supported by evidence @@ -4734,7 +5181,6 @@ class Association(Entity): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ChemicalEntityAssessesNamedThingAssociation(Association): subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") @@ -4775,7 +5221,6 @@ class ChemicalEntityAssessesNamedThingAssociation(Association): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ContributorAssociation(Association): """ Any association between an entity (such as a publication) and various agents that contribute to its realisation @@ -4818,7 +5263,6 @@ class ContributorAssociation(Association): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class GenotypeToGenotypePartAssociation(Association): """ Any association between one genotype and a genotypic entity that is a sub-component of it @@ -4861,7 +5305,6 @@ class GenotypeToGenotypePartAssociation(Association): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class GenotypeToGeneAssociation(Association): """ Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality @@ -4904,7 +5347,6 @@ class GenotypeToGeneAssociation(Association): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class GenotypeToVariantAssociation(Association): """ Any association between a genotype and a sequence variant. @@ -4947,7 +5389,6 @@ class GenotypeToVariantAssociation(Association): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class GeneToGeneAssociation(Association): """ abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction. @@ -4990,7 +5431,6 @@ class GeneToGeneAssociation(Association): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class GeneToGeneHomologyAssociation(GeneToGeneAssociation): """ A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same) @@ -5033,7 +5473,6 @@ class GeneToGeneHomologyAssociation(GeneToGeneAssociation): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class GeneToGeneFamilyAssociation(Association): """ Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships. @@ -5076,7 +5515,6 @@ class GeneToGeneFamilyAssociation(Association): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class GeneExpressionMixin(ConfiguredBaseModel): """ Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the expression occurs. @@ -5087,7 +5525,6 @@ class GeneExpressionMixin(ConfiguredBaseModel): phenotypic_state: Optional[str] = Field(None, description="""in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX.""") - class GeneToGeneCoexpressionAssociation(GeneExpressionMixin, GeneToGeneAssociation): """ Indicates that two genes are co-expressed, generally under the same conditions. @@ -5134,7 +5571,6 @@ class GeneToGeneCoexpressionAssociation(GeneExpressionMixin, GeneToGeneAssociati has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class PairwiseGeneToGeneInteraction(GeneToGeneAssociation): """ An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation) @@ -5177,7 +5613,6 @@ class PairwiseGeneToGeneInteraction(GeneToGeneAssociation): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class PairwiseMolecularInteraction(PairwiseGeneToGeneInteraction): """ An interaction at the molecular level between two physical entities @@ -5221,7 +5656,6 @@ class PairwiseMolecularInteraction(PairwiseGeneToGeneInteraction): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class CellLineToEntityAssociationMixin(ConfiguredBaseModel): """ An relationship between a cell line and another entity @@ -5229,7 +5663,6 @@ class CellLineToEntityAssociationMixin(ConfiguredBaseModel): None - class ChemicalEntityToEntityAssociationMixin(ConfiguredBaseModel): """ An interaction between a chemical entity and another entity @@ -5237,7 +5670,6 @@ class ChemicalEntityToEntityAssociationMixin(ConfiguredBaseModel): None - class DrugToEntityAssociationMixin(ChemicalEntityToEntityAssociationMixin): """ An interaction between a drug and another entity @@ -5245,7 +5677,6 @@ class DrugToEntityAssociationMixin(ChemicalEntityToEntityAssociationMixin): None - class ChemicalToEntityAssociationMixin(ChemicalEntityToEntityAssociationMixin): """ An interaction between a chemical entity and another entity @@ -5253,7 +5684,6 @@ class ChemicalToEntityAssociationMixin(ChemicalEntityToEntityAssociationMixin): None - class CaseToEntityAssociationMixin(ConfiguredBaseModel): """ An abstract association for use where the case is the subject @@ -5261,7 +5691,6 @@ class CaseToEntityAssociationMixin(ConfiguredBaseModel): None - class ChemicalToChemicalAssociation(ChemicalToEntityAssociationMixin, Association): """ A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another. @@ -5304,7 +5733,6 @@ class ChemicalToChemicalAssociation(ChemicalToEntityAssociationMixin, Associatio has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ReactionToParticipantAssociation(ChemicalToChemicalAssociation): stoichiometry: Optional[int] = Field(None, description="""the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers.""") @@ -5348,7 +5776,6 @@ class ReactionToParticipantAssociation(ChemicalToChemicalAssociation): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ReactionToCatalystAssociation(ReactionToParticipantAssociation): stoichiometry: Optional[int] = Field(None, description="""the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers.""") @@ -5392,7 +5819,6 @@ class ReactionToCatalystAssociation(ReactionToParticipantAssociation): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ChemicalToChemicalDerivationAssociation(ChemicalToChemicalAssociation): """ A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: @@ -5443,7 +5869,6 @@ class ChemicalToChemicalDerivationAssociation(ChemicalToChemicalAssociation): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class MolecularActivityToPathwayAssociation(Association): """ Association that holds the relationship between a reaction and the pathway it participates in. @@ -5486,7 +5911,6 @@ class MolecularActivityToPathwayAssociation(Association): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ChemicalToPathwayAssociation(ChemicalToEntityAssociationMixin, Association): """ An interaction between a chemical entity and a biological process or pathway. @@ -5529,7 +5953,6 @@ class ChemicalToPathwayAssociation(ChemicalToEntityAssociationMixin, Association has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class NamedThingAssociatedWithLikelihoodOfNamedThingAssociation(Association): subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") @@ -5570,7 +5993,6 @@ class NamedThingAssociatedWithLikelihoodOfNamedThingAssociation(Association): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ChemicalGeneInteractionAssociation(ChemicalToEntityAssociationMixin, Association): """ describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction) @@ -5621,7 +6043,6 @@ class ChemicalGeneInteractionAssociation(ChemicalToEntityAssociationMixin, Assoc has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ChemicalAffectsGeneAssociation(Association): """ Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity, localization, processing, expression, etc.) @@ -5629,12 +6050,12 @@ class ChemicalAffectsGeneAssociation(Association): subject_form_or_variant_qualifier: Optional[ChemicalOrGeneOrGeneProductFormOrVariantEnum] = Field(None) subject_part_qualifier: Optional[GeneOrGeneProductOrChemicalPartQualifierEnum] = Field(None) subject_derivative_qualifier: Optional[ChemicalEntityDerivativeEnum] = Field(None) - subject_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalPartQualifierEnum] = Field(None) + subject_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalEntityAspectEnum] = Field(None) subject_context_qualifier: Optional[str] = Field(None) subject_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None) object_form_or_variant_qualifier: Optional[ChemicalOrGeneOrGeneProductFormOrVariantEnum] = Field(None) object_part_qualifier: Optional[GeneOrGeneProductOrChemicalPartQualifierEnum] = Field(None) - object_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalPartQualifierEnum] = Field(None) + object_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalEntityAspectEnum] = Field(None) object_context_qualifier: Optional[str] = Field(None) causal_mechanism_qualifier: Optional[CausalMechanismQualifierEnum] = Field(None, description="""A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')""") anatomical_context_qualifier: Optional[str] = Field(None, description="""A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).""") @@ -5677,7 +6098,6 @@ class ChemicalAffectsGeneAssociation(Association): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class DrugToGeneAssociation(DrugToEntityAssociationMixin, Association): """ An interaction between a drug and a gene or gene product. @@ -5720,7 +6140,6 @@ class DrugToGeneAssociation(DrugToEntityAssociationMixin, Association): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class MaterialSampleToEntityAssociationMixin(ConfiguredBaseModel): """ An association between a material sample and something. @@ -5728,7 +6147,6 @@ class MaterialSampleToEntityAssociationMixin(ConfiguredBaseModel): None - class MaterialSampleDerivationAssociation(Association): """ An association between a material sample and the material entity from which it is derived. @@ -5771,13 +6189,11 @@ class MaterialSampleDerivationAssociation(Association): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class DiseaseToEntityAssociationMixin(ConfiguredBaseModel): None - class EntityToExposureEventAssociationMixin(ConfiguredBaseModel): """ An association between some entity and an exposure event. @@ -5785,7 +6201,6 @@ class EntityToExposureEventAssociationMixin(ConfiguredBaseModel): None - class DiseaseToExposureEventAssociation(EntityToExposureEventAssociationMixin, DiseaseToEntityAssociationMixin, Association): """ An association between an exposure event and a disease. @@ -5828,7 +6243,6 @@ class DiseaseToExposureEventAssociation(EntityToExposureEventAssociationMixin, D has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class EntityToOutcomeAssociationMixin(ConfiguredBaseModel): """ An association between some entity and an outcome @@ -5836,7 +6250,6 @@ class EntityToOutcomeAssociationMixin(ConfiguredBaseModel): None - class ExposureEventToOutcomeAssociation(EntityToOutcomeAssociationMixin, Association): """ An association between an exposure event and an outcome. @@ -5881,7 +6294,6 @@ class ExposureEventToOutcomeAssociation(EntityToOutcomeAssociationMixin, Associa has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class FrequencyQualifierMixin(ConfiguredBaseModel): """ Qualifier for frequency type associations @@ -5889,7 +6301,6 @@ class FrequencyQualifierMixin(ConfiguredBaseModel): frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") - class EntityToFeatureOrDiseaseQualifiersMixin(FrequencyQualifierMixin): """ Qualifiers for entity to disease or phenotype associations. @@ -5899,7 +6310,6 @@ class EntityToFeatureOrDiseaseQualifiersMixin(FrequencyQualifierMixin): frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") - class EntityToPhenotypicFeatureAssociationMixin(EntityToFeatureOrDiseaseQualifiersMixin, FrequencyQuantifier): sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") @@ -5912,7 +6322,6 @@ class EntityToPhenotypicFeatureAssociationMixin(EntityToFeatureOrDiseaseQualifie frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") - class InformationContentEntityToNamedThingAssociation(Association): """ association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property). @@ -5955,7 +6364,6 @@ class InformationContentEntityToNamedThingAssociation(Association): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class EntityToDiseaseAssociationMixin(EntityToFeatureOrDiseaseQualifiersMixin): """ mixin class for any association whose object (target node) is a disease @@ -5965,13 +6373,11 @@ class EntityToDiseaseAssociationMixin(EntityToFeatureOrDiseaseQualifiersMixin): frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") - class DiseaseOrPhenotypicFeatureToEntityAssociationMixin(ConfiguredBaseModel): None - class DiseaseOrPhenotypicFeatureToLocationAssociation(DiseaseOrPhenotypicFeatureToEntityAssociationMixin, Association): """ An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site. @@ -6014,7 +6420,6 @@ class DiseaseOrPhenotypicFeatureToLocationAssociation(DiseaseOrPhenotypicFeature has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation(DiseaseOrPhenotypicFeatureToEntityAssociationMixin, Association): """ An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance. @@ -6057,13 +6462,11 @@ class DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation(DiseaseOrPhenoty has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class EntityToDiseaseOrPhenotypicFeatureAssociationMixin(ConfiguredBaseModel): None - class CellLineToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypicFeatureAssociationMixin, CellLineToEntityAssociationMixin, Association): """ An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype. @@ -6106,7 +6509,6 @@ class CellLineToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypi has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ChemicalToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypicFeatureAssociationMixin, ChemicalToEntityAssociationMixin, Association): """ An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype. @@ -6149,7 +6551,6 @@ class ChemicalToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypi has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypicFeatureAssociationMixin, ChemicalToEntityAssociationMixin, Association): """ This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect. @@ -6193,7 +6594,6 @@ class ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation(EntityToD has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation(ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation, EntityToDiseaseOrPhenotypicFeatureAssociationMixin, ChemicalToEntityAssociationMixin): """ This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect. @@ -6237,7 +6637,6 @@ class ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation(C has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class MaterialSampleToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypicFeatureAssociationMixin, MaterialSampleToEntityAssociationMixin, Association): """ An association between a material sample and a disease or phenotype. @@ -6280,13 +6679,11 @@ class MaterialSampleToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhe has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class GenotypeToEntityAssociationMixin(ConfiguredBaseModel): None - class GenotypeToPhenotypicFeatureAssociation(GenotypeToEntityAssociationMixin, EntityToPhenotypicFeatureAssociationMixin, Association): """ Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment @@ -6337,7 +6734,6 @@ class GenotypeToPhenotypicFeatureAssociation(GenotypeToEntityAssociationMixin, E frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") - class ExposureEventToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssociationMixin, Association): """ Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype. @@ -6388,7 +6784,6 @@ class ExposureEventToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssoc frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") - class DiseaseToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssociationMixin, DiseaseToEntityAssociationMixin, Association): """ An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way. @@ -6439,7 +6834,6 @@ class DiseaseToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssociation frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") - class CaseToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssociationMixin, CaseToEntityAssociationMixin, Association): """ An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype. @@ -6490,7 +6884,6 @@ class CaseToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssociationMix frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") - class BehaviorToBehavioralFeatureAssociation(EntityToPhenotypicFeatureAssociationMixin, Association): """ An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior. @@ -6541,13 +6934,11 @@ class BehaviorToBehavioralFeatureAssociation(EntityToPhenotypicFeatureAssociatio frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") - class GeneToEntityAssociationMixin(ConfiguredBaseModel): None - class GeneToPathwayAssociation(GeneToEntityAssociationMixin, Association): """ An interaction between a gene or gene product and a biological process or pathway. @@ -6590,13 +6981,11 @@ class GeneToPathwayAssociation(GeneToEntityAssociationMixin, Association): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class VariantToEntityAssociationMixin(ConfiguredBaseModel): None - class GeneToDiseaseOrPhenotypicFeatureAssociation(GeneToEntityAssociationMixin, EntityToPhenotypicFeatureAssociationMixin, Association): subject_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalEntityAspectEnum] = Field(None) @@ -6647,7 +7036,6 @@ class GeneToDiseaseOrPhenotypicFeatureAssociation(GeneToEntityAssociationMixin, frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") - class GeneToPhenotypicFeatureAssociation(GeneToDiseaseOrPhenotypicFeatureAssociation, GeneToEntityAssociationMixin, EntityToPhenotypicFeatureAssociationMixin): sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") @@ -6698,7 +7086,6 @@ class GeneToPhenotypicFeatureAssociation(GeneToDiseaseOrPhenotypicFeatureAssocia frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") - class GeneToDiseaseAssociation(GeneToDiseaseOrPhenotypicFeatureAssociation, GeneToEntityAssociationMixin, EntityToDiseaseAssociationMixin): subject_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalEntityAspectEnum] = Field(None) @@ -6749,7 +7136,6 @@ class GeneToDiseaseAssociation(GeneToDiseaseOrPhenotypicFeatureAssociation, Gene frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") - class CausalGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityAssociationMixin, EntityToDiseaseAssociationMixin): subject_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalEntityAspectEnum] = Field(None) @@ -6800,7 +7186,6 @@ class CausalGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityAssoc frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") - class CorrelatedGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityAssociationMixin, EntityToDiseaseAssociationMixin): subject_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalEntityAspectEnum] = Field(None) @@ -6851,7 +7236,6 @@ class CorrelatedGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityA frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") - class DruggableGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityAssociationMixin, EntityToDiseaseAssociationMixin): subject_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalEntityAspectEnum] = Field(None) @@ -6902,7 +7286,6 @@ class DruggableGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityAs frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") - class VariantToGeneAssociation(VariantToEntityAssociationMixin, Association): """ An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium) @@ -6945,7 +7328,6 @@ class VariantToGeneAssociation(VariantToEntityAssociationMixin, Association): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class VariantToGeneExpressionAssociation(VariantToGeneAssociation, GeneExpressionMixin): """ An association between a variant and expression of a gene (i.e. e-QTL) @@ -6992,7 +7374,6 @@ class VariantToGeneExpressionAssociation(VariantToGeneAssociation, GeneExpressio has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class VariantToPopulationAssociation(VariantToEntityAssociationMixin, FrequencyQualifierMixin, Association, FrequencyQuantifier): """ An association between a variant and a population, where the variant has particular frequency in the population @@ -7040,7 +7421,6 @@ class VariantToPopulationAssociation(VariantToEntityAssociationMixin, FrequencyQ has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class PopulationToPopulationAssociation(Association): """ An association between a two populations @@ -7083,7 +7463,6 @@ class PopulationToPopulationAssociation(Association): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class VariantToPhenotypicFeatureAssociation(VariantToEntityAssociationMixin, EntityToPhenotypicFeatureAssociationMixin, Association): sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") @@ -7132,7 +7511,6 @@ class VariantToPhenotypicFeatureAssociation(VariantToEntityAssociationMixin, Ent frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") - class VariantToDiseaseAssociation(VariantToEntityAssociationMixin, EntityToDiseaseAssociationMixin, Association): subject: str = Field(..., description="""a sequence variant in which the allele state is associated in some way with the disease state""") @@ -7176,7 +7554,6 @@ class VariantToDiseaseAssociation(VariantToEntityAssociationMixin, EntityToDisea frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") - class GenotypeToDiseaseAssociation(GenotypeToEntityAssociationMixin, EntityToDiseaseAssociationMixin, Association): subject: str = Field(..., description="""a genotype that is associated in some way with a disease state""") @@ -7220,7 +7597,6 @@ class GenotypeToDiseaseAssociation(GenotypeToEntityAssociationMixin, EntityToDis frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") - class ModelToDiseaseAssociationMixin(ConfiguredBaseModel): """ This mixin is used for any association class for which the subject (source node) plays the role of a 'model', in that it recapitulates some features of the disease in a way that is useful for studying the disease outside a patient carrying the disease @@ -7228,7 +7604,6 @@ class ModelToDiseaseAssociationMixin(ConfiguredBaseModel): None - class GeneAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, GeneToDiseaseAssociation, EntityToDiseaseAssociationMixin): subject_aspect_qualifier: Optional[GeneOrGeneProductOrChemicalEntityAspectEnum] = Field(None) @@ -7279,7 +7654,6 @@ class GeneAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, GeneToDis frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") - class VariantAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, VariantToDiseaseAssociation, EntityToDiseaseAssociationMixin): subject: str = Field(..., description="""A variant that has a role in modeling the disease.""") @@ -7323,7 +7697,6 @@ class VariantAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, Varian frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") - class GenotypeAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, GenotypeToDiseaseAssociation, EntityToDiseaseAssociationMixin): subject: str = Field(..., description="""A genotype that has a role in modeling the disease.""") @@ -7367,7 +7740,6 @@ class GenotypeAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, Genot frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") - class CellLineAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, CellLineToDiseaseOrPhenotypicFeatureAssociation, EntityToDiseaseAssociationMixin): subject: str = Field(..., description="""A cell line derived from an organismal entity with a disease state that is used as a model of that disease.""") @@ -7411,7 +7783,6 @@ class CellLineAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, CellL frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") - class OrganismalEntityAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, EntityToDiseaseAssociationMixin, Association): subject: str = Field(..., description="""A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease.""") @@ -7455,7 +7826,6 @@ class OrganismalEntityAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixi frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") - class OrganismToOrganismAssociation(Association): subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") @@ -7496,7 +7866,6 @@ class OrganismToOrganismAssociation(Association): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class TaxonToTaxonAssociation(Association): subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") @@ -7537,7 +7906,6 @@ class TaxonToTaxonAssociation(Association): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class GeneHasVariantThatContributesToDiseaseAssociation(GeneToDiseaseAssociation): subject_form_or_variant_qualifier: Optional[str] = Field(None) @@ -7589,7 +7957,6 @@ class GeneHasVariantThatContributesToDiseaseAssociation(GeneToDiseaseAssociation frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") - class GeneToExpressionSiteAssociation(Association): """ An association between a gene and a gene expression site, possibly qualified by stage/timing info. @@ -7634,7 +8001,6 @@ class GeneToExpressionSiteAssociation(Association): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class SequenceVariantModulatesTreatmentAssociation(Association): """ An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used. @@ -7677,7 +8043,6 @@ class SequenceVariantModulatesTreatmentAssociation(Association): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class FunctionalAssociation(Association): """ An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed. @@ -7720,7 +8085,6 @@ class FunctionalAssociation(Association): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class MacromolecularMachineToEntityAssociationMixin(ConfiguredBaseModel): """ an association which has a macromolecular machine mixin as a subject @@ -7728,7 +8092,6 @@ class MacromolecularMachineToEntityAssociationMixin(ConfiguredBaseModel): None - class MacromolecularMachineToMolecularActivityAssociation(MacromolecularMachineToEntityAssociationMixin, FunctionalAssociation): """ A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution. @@ -7771,7 +8134,6 @@ class MacromolecularMachineToMolecularActivityAssociation(MacromolecularMachineT has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class MacromolecularMachineToBiologicalProcessAssociation(MacromolecularMachineToEntityAssociationMixin, FunctionalAssociation): """ A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it. @@ -7814,7 +8176,6 @@ class MacromolecularMachineToBiologicalProcessAssociation(MacromolecularMachineT has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class MacromolecularMachineToCellularComponentAssociation(MacromolecularMachineToEntityAssociationMixin, FunctionalAssociation): """ A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component. @@ -7857,7 +8218,6 @@ class MacromolecularMachineToCellularComponentAssociation(MacromolecularMachineT has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class MolecularActivityToChemicalEntityAssociation(Association): """ Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples @@ -7900,7 +8260,6 @@ class MolecularActivityToChemicalEntityAssociation(Association): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class MolecularActivityToMolecularActivityAssociation(Association): """ Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples @@ -7943,7 +8302,6 @@ class MolecularActivityToMolecularActivityAssociation(Association): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class GeneToGoTermAssociation(FunctionalAssociation): subject: str = Field(..., description="""gene, product or macromolecular complex that has the function associated with the GO term""") @@ -7984,7 +8342,6 @@ class GeneToGoTermAssociation(FunctionalAssociation): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class EntityToDiseaseAssociation(Association): FDA_approval_status: Optional[FDAApprovalStatusEnum] = Field(None) @@ -8026,7 +8383,6 @@ class EntityToDiseaseAssociation(Association): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class EntityToPhenotypicFeatureAssociation(Association): FDA_approval_status: Optional[FDAApprovalStatusEnum] = Field(None) @@ -8068,7 +8424,6 @@ class EntityToPhenotypicFeatureAssociation(Association): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class SequenceAssociation(Association): """ An association between a sequence feature and a nucleic acid entity it is localized to. @@ -8111,7 +8466,6 @@ class SequenceAssociation(Association): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class GenomicSequenceLocalization(SequenceAssociation): """ A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig. @@ -8159,7 +8513,6 @@ class GenomicSequenceLocalization(SequenceAssociation): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class SequenceFeatureRelationship(Association): """ For example, a particular exon is part of a particular transcript or gene @@ -8202,7 +8555,6 @@ class SequenceFeatureRelationship(Association): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class TranscriptToGeneRelationship(SequenceFeatureRelationship): """ A gene is a collection of transcripts @@ -8245,7 +8597,6 @@ class TranscriptToGeneRelationship(SequenceFeatureRelationship): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class GeneToGeneProductRelationship(SequenceFeatureRelationship): """ A gene is transcribed and potentially translated to a gene product @@ -8288,7 +8639,6 @@ class GeneToGeneProductRelationship(SequenceFeatureRelationship): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ExonToTranscriptRelationship(SequenceFeatureRelationship): """ A transcript is formed from multiple exons @@ -8331,7 +8681,6 @@ class ExonToTranscriptRelationship(SequenceFeatureRelationship): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation(Association): """ A regulatory relationship between two genes @@ -8375,7 +8724,6 @@ class ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation(Association): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class AnatomicalEntityToAnatomicalEntityAssociation(Association): subject: str = Field(..., description="""connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") @@ -8416,7 +8764,6 @@ class AnatomicalEntityToAnatomicalEntityAssociation(Association): has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class AnatomicalEntityToAnatomicalEntityPartOfAssociation(AnatomicalEntityToAnatomicalEntityAssociation): """ A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms @@ -8459,7 +8806,6 @@ class AnatomicalEntityToAnatomicalEntityPartOfAssociation(AnatomicalEntityToAnat has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class AnatomicalEntityToAnatomicalEntityOntogenicAssociation(AnatomicalEntityToAnatomicalEntityAssociation): """ A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship. @@ -8502,7 +8848,6 @@ class AnatomicalEntityToAnatomicalEntityOntogenicAssociation(AnatomicalEntityToA has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class OrganismTaxonToEntityAssociation(ConfiguredBaseModel): """ An association between an organism taxon and another entity @@ -8510,7 +8855,6 @@ class OrganismTaxonToEntityAssociation(ConfiguredBaseModel): None - class OrganismTaxonToOrganismTaxonAssociation(OrganismTaxonToEntityAssociation, Association): """ A relationship between two organism taxon nodes @@ -8553,7 +8897,6 @@ class OrganismTaxonToOrganismTaxonAssociation(OrganismTaxonToEntityAssociation, has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class OrganismTaxonToOrganismTaxonSpecialization(OrganismTaxonToOrganismTaxonAssociation): """ A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo @@ -8596,7 +8939,6 @@ class OrganismTaxonToOrganismTaxonSpecialization(OrganismTaxonToOrganismTaxonAss has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class OrganismTaxonToOrganismTaxonInteraction(OrganismTaxonToOrganismTaxonAssociation): """ An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens @@ -8640,7 +8982,6 @@ class OrganismTaxonToOrganismTaxonInteraction(OrganismTaxonToOrganismTaxonAssoci has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - class OrganismTaxonToEnvironmentAssociation(OrganismTaxonToEntityAssociation, Association): subject: str = Field(..., description="""the taxon that is the subject of the association""") @@ -8682,13 +9023,11 @@ class OrganismTaxonToEnvironmentAssociation(OrganismTaxonToEntityAssociation, As - # Update forward refs # see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ -GenomeAssembly.update_forward_refs() -Mapping.update_forward_refs() -Mappings.update_forward_refs() AnnotationCollection.update_forward_refs() +ProvActivity.update_forward_refs() +ProvEntity.update_forward_refs() MappingCollection.update_forward_refs() PredicateMapping.update_forward_refs() OntologyClass.update_forward_refs() @@ -8702,6 +9041,16 @@ class OrganismTaxonToEnvironmentAssociation(OrganismTaxonToEntityAssociation, As ChemicalOrDrugOrTreatment.update_forward_refs() Entity.update_forward_refs() Checksum.update_forward_refs() +BrainSegment.update_forward_refs() +BrainSection.update_forward_refs() +TissueSample.update_forward_refs() +DissociatedCellSample.update_forward_refs() +EnrichedCellSample.update_forward_refs() +BarcodedCellSample.update_forward_refs() +AmplifiedCdna.update_forward_refs() +Library.update_forward_refs() +LibraryAliquot.update_forward_refs() +LibraryPool.update_forward_refs() NamedThing.update_forward_refs() Attribute.update_forward_refs() ChemicalRole.update_forward_refs() @@ -8748,6 +9097,16 @@ class OrganismTaxonToEnvironmentAssociation(OrganismTaxonToEntityAssociation, As Occurrent.update_forward_refs() ActivityAndBehavior.update_forward_refs() Activity.update_forward_refs() +BrainExtraction.update_forward_refs() +BrainSegmentSectioning.update_forward_refs() +TissueDissecting.update_forward_refs() +CellDissociation.update_forward_refs() +CellEnrichment.update_forward_refs() +CellBarcoding.update_forward_refs() +CdnaAmplification.update_forward_refs() +LibraryConstruction.update_forward_refs() +LibraryAliquoting.update_forward_refs() +LibraryPooling.update_forward_refs() Study.update_forward_refs() Procedure.update_forward_refs() Phenomenon.update_forward_refs() @@ -8761,6 +9120,8 @@ class OrganismTaxonToEnvironmentAssociation(OrganismTaxonToEntityAssociation, As GeographicLocation.update_forward_refs() GeographicLocationAtTime.update_forward_refs() ThingWithTaxon.update_forward_refs() +GenomeAssembly.update_forward_refs() +Donor.update_forward_refs() BiologicalEntity.update_forward_refs() GenomicEntity.update_forward_refs() EpigenomicEntity.update_forward_refs()