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bioschemasdrafts.json
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bioschemasdrafts.json
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{
"@context": {
"schema": "http://schema.org/",
"rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdfs": "http://www.w3.org/2000/01/rdf-schema#",
"owl": "http://www.w3.org/2002/07/owl/",
"bioschemas": "https://discovery.biothings.io/view/bioschemas/",
"bioschemasdrafts": "https://discovery.biothings.io/view/bioschemasdrafts/",
"bioschemastypes": "https://discovery.biothings.io/view/bioschemastypes/",
"bioschemastypesdrafts": "https://discovery.biothings.io/view/bioschemastypesdrafts/",
"bioschemasdeprecated": "https://discovery.biothings.io/view/bioschemasdeprecated/",
"dct": "http://purl.org/dc/terms/",
"@dateModified": "01/19/2024, 16:03:04",
"dwc": "http://rs.tdwg.org/dwc/terms/",
"ppeo:hasGrowthFacility": "http://purl.org/ppeo/PPEO.owl#hasGrowthFacility"
},
"@graph": [
{
"@id": "bioschemasdrafts:Gene",
"@type": "rdfs:Class",
"rdfs:comment": "This Gene profile specification presents the markup for describing a Gene. Version 1.1-DRAFT. <h3>Summary of Changes</h3> Changes since 1.0-RELEASE: <ul><li>Updated type properties to Schema.org pending release.</li><li>Addition of hasSequenceAnnotation property at Recommended level.</li><li>Added sameAs as recommended.</li><li>Remove use of mainEntityOfPage; DataRecord has been deprecated. </li></ul>",
"rdfs:label": "Gene",
"rdfs:subClassOf": {
"@id": "schema:Gene"
},
"$validation": {
"$schema": "http://json-schema.org/draft-07/schema#",
"type": "object",
"properties": {
"identifier": {
"description": "The identifier property represents any kind of identifier for any kind of <a class=\"localLink\" href=\"http://schema.org/Thing\">Thing</a>, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See <a href=\"/docs/datamodel.html#identifierBg\">background notes</a> for more details.",
"anyOf": [
{
"$ref": "#/definitions/propertyValue"
},
{
"type": "string"
},
{
"type": "string",
"format": "uri"
}
],
"owl:cardinality": "one"
},
"name": {
"description": "The name of the item.",
"type": "string",
"owl:cardinality": "one"
},
"description": {
"description": "A description of the item.",
"type": "string",
"owl:cardinality": "one"
},
"encodesBioChemEntity": {
"description": "For genes, this property is used to express in a generic way gene products encoded by this gene, for instance RNA or Protein",
"oneOf": [
{
"$ref": "#/definitions/bioChemEntity"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/bioChemEntity"
}
}
],
"owl:cardinality": "many"
},
"hasSequenceAnnotation": {
"description": "The taxonomic grouping of the organism that expresses, encodes, or in someway related to the BioChemEntity.",
"anyOf": [
{
"$ref": "#/definitions/sequenceAnnotation"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/sequenceAnnotation"
}
},
{
"type": "string",
"format": "uri"
},
{
"type": "array",
"items": {
"type": "string",
"format": "uri"
}
}
],
"owl:cardinality": "many"
},
"isPartOfBioChemEntity": {
"description": "Indicates a BioChemEntity that is (in some sense) a part of this BioChemEntity. Inverse property: hasBioChemEntityPart. For genes, it is recommended to at least specify the DNA/chromosome containing this gene.",
"oneOf": [
{
"$ref": "#/definitions/bioChemEntity"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/bioChemEntity"
}
}
],
"owl:cardinality": "many"
},
"url": {
"description": "URL of the item.",
"type": "string",
"format": "uri",
"owl:cardinality": "one"
},
"alternateName": {
"description": "An alias for the item.",
"oneOf": [
{
"type": "string"
},
{
"type": "array",
"items": {
"type": "string"
}
}
],
"owl:cardinality": "many"
},
"alternativeOf": {
"description": "Is variant of. Use this property to express when a gene is a variant of any other gene.",
"oneOf": [
{
"$ref": "#/definitions/gene"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/gene"
}
}
],
"owl:cardinality": "many"
},
"associatedDisease": {
"description": "Disease associated to this BioChemEntity. Such a disease can be a MedicalCondition or a URL. If you want to add an evidence supporting the association, please use PropertyValue.",
"anyOf": [
{
"$ref": "#/definitions/medicalCondition"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/medicalCondition"
}
},
{
"$ref": "#/definitions/propertyValue"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/propertyValue"
}
},
{
"type": "string",
"format": "uri"
},
{
"type": "array",
"items": {
"type": "string",
"format": "uri"
}
}
],
"owl:cardinality": "many"
},
"expressedIn": {
"description": "Tissue, organ, biological sample, etc in which activity of this gene has been observed experimentally. For example brain, digestive system.",
"anyOf": [
{
"$ref": "#/definitions/definedTerm"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/definedTerm"
}
},
{
"$ref": "#/definitions/bioChemEntity"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/bioChemEntity"
}
},
{
"$ref": "#/definitions/anatomicalStructure"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/anatomicalStructure"
}
},
{
"$ref": "#/definitions/anatomicalSystem"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/anatomicalSystem"
}
}
],
"owl:cardinality": "many"
},
"hasBioChemEntityPart": {
"description": "Indicates a BioChemEntity that (in some sense) has this BioChemEntity as a part. Inverse property: isPartOfBioChemEntity",
"oneOf": [
{
"$ref": "#/definitions/bioChemEntity"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/bioChemEntity"
}
}
],
"owl:cardinality": "many"
},
"hasBioPolymerSequence": {
"description": "Schema: A symbolic representation of a BioChemEnity. For example, a nucleotide sequence of a Gene or an amino acid sequence of a Protein.",
"type": "string",
"owl:cardinality": "one"
},
"hasMolecularFunction": {
"description": "Molecular function performed by this BioChemEntity; please use PropertyValue if you want to include any evidence.",
"anyOf": [
{
"$ref": "#/definitions/definedTerm"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/definedTerm"
}
},
{
"$ref": "#/definitions/propertyValue"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/propertyValue"
}
},
{
"type": "string",
"format": "uri"
},
{
"type": "array",
"items": {
"type": "string",
"format": "uri"
}
}
],
"owl:cardinality": "many"
},
"hasRepresentation": {
"description": "A common representation such as a protein sequence or chemical structure for this entity. For images use schema.org/image.",
"anyOf": [
{
"$ref": "#/definitions/propertyValue"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/propertyValue"
}
},
{
"type": "string"
},
{
"type": "array",
"items": {
"type": "string"
}
},
{
"type": "string",
"format": "uri"
},
{
"type": "array",
"items": {
"type": "string",
"format": "uri"
}
}
],
"owl:cardinality": "many"
},
"hasStatus": {
"description": "Schema: One of pseudogene, dead, killed, live, predicted, suppressed.",
"type": "string",
"enum": [
"pseudogene",
"dead",
"killed",
"live",
"predicted",
"suppressed"
],
"owl:cardinality": "one"
},
"image": {
"description": "An image of the item. This can be a <a class=\"localLink\" href=\"http://schema.org/URL\">URL</a> or a fully described <a class=\"localLink\" href=\"http://schema.org/ImageObject\">ImageObject</a>.",
"type": "string",
"format": "uri",
"owl:cardinality": "one"
},
"isInvolvedInBiologicalProcess": {
"description": "Biological process this BioChemEntity is involved in; please use PropertyValue if you want to include any evidence.",
"anyOf": [
{
"$ref": "#/definitions/definedTerm"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/definedTerm"
}
},
{
"$ref": "#/definitions/propertyValue"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/propertyValue"
}
},
{
"type": "string",
"format": "uri"
},
{
"type": "array",
"items": {
"type": "string",
"format": "uri"
}
}
],
"owl:cardinality": "many"
},
"isLocatedInSubcellularLocation": {
"description": "Subcellular location where this BioChemEntity is located; please use PropertyValue if you want to include any evidence.",
"anyOf": [
{
"$ref": "#/definitions/definedTerm"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/definedTerm"
}
},
{
"$ref": "#/definitions/propertyValue"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/propertyValue"
}
},
{
"type": "string",
"format": "uri"
},
{
"type": "array",
"items": {
"type": "string",
"format": "uri"
}
}
],
"owl:cardinality": "many"
},
"mainEntityOfPage": {
"description": "Indicates a page (or other CreativeWork) for which this thing is the main entity being described. See <a href=\"/docs/datamodel.html#mainEntityBackground\">background notes</a> for details.",
"type": "string",
"format": "uri",
"owl:cardinality": "one"
},
"sameAs": {
"description": "URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.",
"type": "string",
"format": "uri",
"owl:cardinality": "one"
},
"taxonomicRange": {
"description": "The taxonomic grouping of the organism that expresses, encodes, or in someway related to the BioChemEntity.",
"anyOf": [
{
"$ref": "#/definitions/definedTerm"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/definedTerm"
}
},
{
"$ref": "#/definitions/taxon"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/taxon"
}
},
{
"type": "string"
},
{
"type": "array",
"items": {
"type": "string"
}
},
{
"type": "string",
"format": "uri"
},
{
"type": "array",
"items": {
"type": "string",
"format": "uri"
}
}
],
"owl:cardinality": "many"
},
"conformsTo": {
"description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/blob/master/Gene/jsonld/Gene_v1.1-DRAFT.json",
"$ref": "#/definitions/conformsDefinition"
}
},
"required": [
"identifier",
"name",
"conformsTo"
],
"recommended": [
"description",
"encodesBioChemEntity",
"isPartOfBioChemEntity",
"url",
"hasSequenceAnnotation",
"sameAs"
],
"optional": [
"alternateName",
"alternativeOf",
"associatedDisease",
"expressedIn",
"hasBioChemEntityPart",
"hasBioPolymerSequence",
"hasMolecularFunction",
"hasRepresentation",
"hasStatus",
"image",
"isInvolvedInBiologicalProcess",
"isLocatedInSubcellularLocation",
"mainEntityOfPage",
"taxonomicRange"
],
"definitions": {
"taxon": {
"@type": "Taxon",
"type": "object",
"properties": {
"name": {
"type": "string"
},
"taxonRank": {
"anyOf": [
{
"$ref": "#/definitions/propertyValue"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/propertyValue"
}
},
{
"type": "string"
},
{
"type": "array",
"items": {
"type": "string"
}
},
{
"type": "string",
"format": "uri"
},
{
"type": "array",
"items": {
"type": "string",
"format": "uri"
}
}
]
}
},
"required": [
"name",
"taxonRank"
]
},
"propertyValue": {
"@type": "PropertyValue",
"type": "object",
"properties": {
"name": {
"type": "string"
},
"value": {
"type": "string"
}
},
"required": []
},
"definedTerm": {
"@type": "DefinedTerm",
"type": "object",
"properties": {
"url": {
"type": "string",
"format": "uri"
},
"name": {
"type": "string"
},
"termCode": {
"type": "string"
}
},
"required": []
},
"medicalCondition": {
"@type": "MedicalCondition",
"type": "object",
"properties": {
"url": {
"type": "string",
"format": "uri"
},
"name": {
"type": "string"
}
},
"required": []
},
"bioChemEntity": {
"@type": "BioChemEntity",
"type": "object",
"properties": {
"url": {
"type": "string",
"format": "uri"
},
"name": {
"type": "string"
}
},
"required": []
},
"gene": {
"@type": "Gene",
"type": "object",
"properties": {
"identifier": {
"anyOf": [
{
"$ref": "#/definitions/propertyValue"
},
{
"type": "string"
},
{
"type": "string",
"format": "uri"
}
]
},
"name": {
"type": "string"
}
},
"required": []
},
"quantitativeValue": {
"@type": "QuantitativeValue",
"type": "object",
"properties": {
"value": {
"type": "string"
},
"unitText": {
"type": "string"
}
},
"required": []
},
"anatomicalStructure": {
"@type": "AnatomicalStructure",
"type": "object",
"properties": {
"name": {
"type": "string"
}
},
"required": []
},
"anatomicalSystem": {
"@type": "AnatomicalSystem",
"type": "object",
"properties": {
"name": {
"type": "string"
}
},
"required": []
},
"sequenceAnnotation": {
"@type": "bioschemastypesdrafts:SequenceAnnotation",
"type": "object",
"properties": {
"sequenceLocation": {
"$ref": "#/definitions/sequenceRange"
}
},
"required": []
},
"sequenceRange": {
"@type": "bioschemastypesdrafts:SequenceRange",
"type": "object",
"properties": {
"rangeStart": {
"type": "integer"
}
},
"required": []
},
"conformsDefinition": {
"@type": "CreativeWork",
"type": "object",
"properties": {
"identifier": {
"description": "The url of the version bioschemas profile that was used. For jsonschema, set @id to the identifier",
"oneOf": [
{
"enum": [
"https://github.com/BioSchemas/specifications/blob/master/Gene/jsonld/Gene_v1.1-DRAFT.json"
]
},
{
"type": "string",
"format": "uri"
}
]
}
},
"required": [
"identifier"
]
}
}
},
"additional_type": "https://bioschemas.org/profiles#nav-draft",
"schema:schemaVersion": [
"https://bioschemas.org/profiles/Gene/1.1-DRAFT",
"https://github.com/BioSchemas/specifications/blob/master/Gene/jsonld/Gene_v1.1-DRAFT.json"
]
},
{
"@id": "bioschemasdrafts:Taxon",
"@type": "rdfs:Class",
"rdfs:comment": "Bioschemas profile for describing a biological taxon This profile aims to denote a taxon by common properties such as its scientific name, taxonomic rank and vernacular names. It is also a means to link to existing taxonomic registers where each taxon has a URI. Version 0.8-DRAFT.<br/><h3>Summary of Changes</h3><br>Changes since 0.7-DRAFT:<ul><li>Change sameAs from optional to recommended.</li></ul>",
"schema:schemaVersion": [
"https://bioschemas.org/profiles/Taxon/0.8-DRAFT",
"https://github.com/BioSchemas/specifications/tree/master/Taxon/jsonld/Taxon_v0.8-DRAFT.json"
],
"rdfs:label": "Taxon",
"rdfs:subClassOf": {
"@id": "schema:Taxon"
},
"$validation": {
"$schema": "http://json-schema.org/draft-07/schema#",
"type": "object",
"properties": {
"additionalType": {
"description": "A Taxon type from a well known vocabulary, e.g. DarwinCore http://rs.tdwg.org/dwc/terms/Taxon or http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept An additional type for the item, typically used for adding more specific types from external vocabularies in microdata syntax. This is a relationship between something and a class that the thing is in. In RDFa syntax, it is better to use the native RDFa syntax - the 'typeof' attribute - for multiple types. Schema.org tools may have only weaker understanding of extra types, in particular those defined externally.",
"oneOf": [
{
"type": "string",
"format": "uri"
},
{
"type": "array",
"items": {
"type": "string",
"format": "uri"
}
}
],
"owl:cardinality": "many"
},
"alternateName": {
"description": "Scientific name, with authorship and date information if known, of a synonym of the currently valid (zoological) or accepted (botanical) name. An alias for the item.",
"oneOf": [
{
"type": "string"
},
{
"type": "array",
"items": {
"type": "string"
}
}
],
"owl:cardinality": "many"
},
"alternateScientificName": {
"description": " A TaxonName representing a scientific name, with authorship and date information if known, of a synonym of the currently valid (zoological) or accepted (botanical) name",
"oneOf": [
{
"$ref": "#/definitions/taxonname"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/taxonname"
}
}
],
"owl:cardinality": "many"
},
"childTaxon": {
"description": "Direct, most proximate lower-rank child taxa Closest child taxa of the taxon in question.\nInverse property: parentTaxon",
"anyOf": [
{
"$ref": "#/definitions/taxon"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/taxon"
}
},
{
"type": "string"
},
{
"type": "array",
"items": {
"type": "string"
}
},
{
"type": "string",
"format": "uri"
},
{
"type": "array",
"items": {
"type": "string",
"format": "uri"
}
}
],
"owl:cardinality": "many"
},
"description": {
"description": " A description of the item.",
"type": "string",
"owl:cardinality": "one"
},
"disambiguatingDescription": {
"description": "Can be used to specify the taxon circumscription retained in this description, e.g. by denoting the scientific works that assert the status of the accepted/valid name and synonyms. A sub property of description. A short description of the item used to disambiguate from other, similar items. Information from other properties (in particular, name) may be necessary for the description to be useful for disambiguation.",
"type": "string",
"owl:cardinality": "one"
},
"vernacularName": {
"description": "A vernacular (common) name of the taxon ",
"oneOf": [
{
"type": "string"
},
{
"type": "array",
"items": {
"type": "string"
}
}
],
"owl:cardinality": "many"
},
"identifier": {
"description": "A PropertyValue should be used to relate the taxon with couterparts identifiers within well known authorities such as GBIF, WoRMS, EoL etc.\nWikidata properties may be used in this respect, e.g.:\nNCBI id (https://www.wikidata.org/entity/P685), \nGBIF id (https://www.wikidata.org/entity/P846),\nEoL id (https://www.wikidata.org/entity/P830), \niNaturalist id (https://www.wikidata.org/entity/P3151), \nWoRMS id (https://www.wikidata.org/entity/P850), \nFishbase id (https://www.wikidata.org/entity/P938),\nTAXREF id (https://www.wikidata.org/entity/P3186),\n...\n The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See [background notes](http://schema.org/docs/datamodel.html#identifierBg) for more details.\n",
"oneOf": [
{
"$ref": "#/definitions/propertyvalue"
},
{
"type": "string"
},
{
"type": "string",
"format": "uri"
}
],
"owl:cardinality": "one"
},
"image": {
"description": " An image of the item. This can be a URL or a fully described ImageObject.",
"oneOf": [
{
"$ref": "#/definitions/imageobject"
},
{
"type": "string",
"format": "uri"
}
],
"owl:cardinality": "one"
},
"isBasedOn": {
"description": "A CreativeWork, such as a scholarly article, asserting the status of the accepted/valid name and synonyms, retained for the taxon circumscription A resource from which this work is derived or from which it is a modification or adaption. Supersedes, isBasedOnUrl. ",
"oneOf": [
{
"$ref": "#/definitions/creativework"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/creativework"
}
}
],
"owl:cardinality": "many"
},
"mainEntityOfPage": {
"description": " Indicates a page (or other CreativeWork) for which this thing is the main entity being described. See background notes for details.\nInverse property: mainEntity.",
"oneOf": [
{
"$ref": "#/definitions/creativework"
},
{
"type": "string",
"format": "uri"
}
],
"owl:cardinality": "one"
},
"name": {
"description": "Currently valid (zoological) or accepted (botanical) name for that taxon, with authorship and date information if known. The name of the item.",
"type": "string",
"owl:cardinality": "one"
},
"parentTaxon": {
"description": "Direct, most proximate higher-rank parent taxon Closest parent taxon of the taxon in question.\nInverse property: childTaxon",
"oneOf": [
{
"$ref": "#/definitions/taxon"
},
{
"type": "string"
},
{
"type": "string",
"format": "uri"
}
],
"owl:cardinality": "one"
},
"sameAs": {
"description": "URL of third-party webpages describing the same taxon URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.",
"oneOf": [
{
"type": "string",
"format": "uri"
},
{
"type": "array",
"items": {
"type": "string",
"format": "uri"
}
}
],
"owl:cardinality": "many"
},
"scientificName": {
"description": " A TaxonName representing the currently valid (zoological) or accepted (botanical) name for that taxon",
"$ref": "#/definitions/taxonname",
"owl:cardinality": "one"
},
"taxonRank": {
"description": " The taxonomic rank of this taxon given preferably as a URI from a controlled vocabulary (e.g. the ranks from TDWG TaxonRank ontology or equivalent Wikidata URIs)",
"anyOf": [
{
"$ref": "#/definitions/propertyvalue"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/propertyvalue"
}
},
{
"type": "string"
},
{
"type": "array",
"items": {
"type": "string"
}
},
{
"type": "string",
"format": "uri"
},
{
"type": "array",
"items": {
"type": "string",
"format": "uri"
}
}
],
"owl:cardinality": "many"
},
"url": {
"description": "Link to the webpage associated to this taxon URL of the item.",
"type": "string",
"format": "uri",
"owl:cardinality": "one"
},
"conformsTo": {
"description": "This is used to state the Bioschemas profile that the markup relates to. The identifier can be the url for the version of this bioschemas class on github: https://github.com/BioSchemas/specifications/tree/master/Taxon/jsonld/Taxon_v0.8-DRAFT.json",
"$ref": "#/definitions/conformsDefinition"
}
},
"required": [
"name",
"taxonRank",
"conformsTo"
],
"recommended": [
"parentTaxon",
"scientificName",
"url",
"sameAs"
],
"optional": [
"additionalType",
"alternateName",
"alternateScientificName",
"childTaxon",
"description",
"disambiguatingDescription",
"vernacularName",
"identifier",
"image",
"isBasedOn",
"mainEntityOfPage"
],
"definitions": {