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condition-schema.json
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condition-schema.json
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{
"type" : "object",
"id" : "urn:jsonschema:org:phenopackets:api:model:condition:Condition",
"properties" : {
"types" : {
"type" : "array",
"description" : "Any instance can be positively described as the intersection of any number of ontology classes.",
"items" : {
"type" : "object",
"id" : "urn:jsonschema:org:phenopackets:api:model:ontology:OntologyClass",
"properties" : {
"id" : {
"type" : "string",
"description" : "A unique ontology class identifier, can be either URI or CURIE"
},
"label" : {
"type" : "string",
"description" : "A string that contains the preferred natural language term to denote the class"
}
}
}
},
"negated_types" : {
"type" : "array",
"description" : "Any instance can be assigned any number of negative classes.",
"items" : {
"type" : "object",
"$ref" : "urn:jsonschema:org:phenopackets:api:model:ontology:OntologyClass"
}
},
"description" : {
"type" : "string",
"description" : "An optional free text description that can enhance the ontology class based description"
},
"has_location" : {
"type" : "object",
"id" : "urn:jsonschema:org:phenopackets:api:model:condition:OrganismalSite",
"description" : "the location in an organism or cell in which the phenotype manifests",
"properties" : {
"types" : {
"type" : "array",
"description" : "Any instance can be positively described as the intersection of any number of ontology classes.",
"items" : {
"type" : "object",
"$ref" : "urn:jsonschema:org:phenopackets:api:model:ontology:OntologyClass"
}
},
"negated_types" : {
"type" : "array",
"description" : "Any instance can be assigned any number of negative classes.",
"items" : {
"type" : "object",
"$ref" : "urn:jsonschema:org:phenopackets:api:model:ontology:OntologyClass"
}
},
"description" : {
"type" : "string",
"description" : "An optional free text description that can enhance the ontology class based description"
}
}
},
"onset" : {
"type" : "object",
"id" : "urn:jsonschema:org:phenopackets:api:model:condition:TemporalRegion",
"description" : "the time region in which the condition is first manifest",
"properties" : {
"types" : {
"type" : "array",
"description" : "Any instance can be positively described as the intersection of any number of ontology classes.",
"items" : {
"type" : "object",
"$ref" : "urn:jsonschema:org:phenopackets:api:model:ontology:OntologyClass"
}
},
"negated_types" : {
"type" : "array",
"description" : "Any instance can be assigned any number of negative classes.",
"items" : {
"type" : "object",
"$ref" : "urn:jsonschema:org:phenopackets:api:model:ontology:OntologyClass"
}
},
"description" : {
"type" : "string",
"description" : "An optional free text description that can enhance the ontology class based description"
},
"start_time" : {
"type" : "string",
"description" : "the date or time at which the interval starts"
},
"end_time" : {
"type" : "string",
"description" : "the date or time at which the interval ends"
}
}
},
"offset" : {
"type" : "object",
"$ref" : "urn:jsonschema:org:phenopackets:api:model:condition:TemporalRegion",
"description" : "the time region in which the condition ceases to manifest"
},
"severity" : {
"type" : "object",
"id" : "urn:jsonschema:org:phenopackets:api:model:condition:ConditionSeverity",
"description" : "the degree to which the phenotype is manifest, related to the concept of expressivity, see http:https://www.ncbi.nlm.nih.gov/books/NBK22090/",
"properties" : {
"types" : {
"type" : "array",
"description" : "Any instance can be positively described as the intersection of any number of ontology classes.",
"items" : {
"type" : "object",
"$ref" : "urn:jsonschema:org:phenopackets:api:model:ontology:OntologyClass"
}
},
"negated_types" : {
"type" : "array",
"description" : "Any instance can be assigned any number of negative classes.",
"items" : {
"type" : "object",
"$ref" : "urn:jsonschema:org:phenopackets:api:model:ontology:OntologyClass"
}
},
"description" : {
"type" : "string",
"description" : "An optional free text description that can enhance the ontology class based description"
}
}
},
"environment" : {
"type" : "object",
"id" : "urn:jsonschema:org:phenopackets:api:model:environment:Environment",
"description" : "the environment in which the phenotype is expressed",
"properties" : {
"types" : {
"type" : "array",
"description" : "Any instance can be positively described as the intersection of any number of ontology classes.",
"items" : {
"type" : "object",
"$ref" : "urn:jsonschema:org:phenopackets:api:model:ontology:OntologyClass"
}
},
"negated_types" : {
"type" : "array",
"description" : "Any instance can be assigned any number of negative classes.",
"items" : {
"type" : "object",
"$ref" : "urn:jsonschema:org:phenopackets:api:model:ontology:OntologyClass"
}
},
"description" : {
"type" : "string",
"description" : "An optional free text description that can enhance the ontology class based description"
}
}
}
}
}