Gene_v1.1-DRAFT.json

{
    "@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#",
        "bioschemastypesdrafts": "https://discovery.biothings.io/view/bioschemastypesdrafts/",
        "bioschemasdrafts": "https://discovery.biothings.io/view/bioschemasdrafts/",
        "owl": "http://www.w3.org/2002/07/owl/"
    },
    "@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"
                    }
                },
                "required": [
                    "identifier",
                    "name"
                ],
                "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": []
                    }
                }
            }
        },
        {
            "@id": "bioschemasdrafts:hasStatus",
            "rdfs:comment": "One of pseudogene, dead, killed, live, predicted, suppressed.",
            "@type": "rdf:Property",
            "rdfs:label": "hasStatus",
            "schema:domainIncludes": {
                "@id": "bioschemasdrafts:Gene"
            },
            "schema:rangeIncludes": [
                {
                    "@id": "schema:Text"
                }
            ]
        },
        {
            "@id": "bioschemasdrafts:hasSequenceAnnotation",
            "rdfs:comment": "An annotation on the BioPolymerSequence associated with this BioChemEntity. For genes, it can be used to link to gene sequence annotations such as variants or so.",
            "@type": "rdf:Property",
            "rdfs:label": "hasSequenceAnnotation",
            "schema:domainIncludes": {
                "@id": "bioschemasdrafts:Gene"
            },
            "schema:rangeIncludes": [
                {
                    "@id": "bioschemastypesdrafts:SequenceAnnotation"
                },
                {
                    "@id": "schema:URL"
                }
            ]
        }
    ]
}