|
{
"additionalProperties" : false ,
"description" : "JSON Schema for Convert-Pheno mapping file" ,
"type" : "object" ,
"required" : [
"project" ,
"id" ,
"sex"
],
"properties" : {
"project" : {
"type" : "object" ,
"required" : [
"id" ,
"source" ,
"ontology" ,
"version" ,
"baselineFieldsToPropagate"
],
"properties" : {
"id" : {
"$ref" : "#/$defs/stringField"
},
"source" : {
"type" : "string" ,
"enum" : [
"redcap" ,
"cdisc-odm" ,
"csv"
]
},
"ontology" : {
"$ref" : "#/$defs/objectField/properties/ontology"
},
"version" : {
"$ref" : "#/$defs/stringField"
},
"description" : {
"$ref" : "#/$defs/stringField"
},
"baselineFieldsToPropagate" : {
"$ref" : "#/$defs/arrayField"
}
}
},
"diseases" : {
"$ref" : "#/$defs/objectField"
},
"ethnicity" : {
"$ref" : "#/$defs/objectField"
},
"exposures" : {
"$ref" : "#/$defs/objectField"
},
"geographicOrigin" : {
"$ref" : "#/$defs/stringField"
},
"id" : {
"$ref" : "#/$defs/objectField"
},
"info" : {
"$ref" : "#/$defs/objectField"
},
"interventionsOrProcedures" : {
"$ref" : "#/$defs/objectField"
},
"karyotypicSex" : {
"$ref" : "#/$defs/stringField"
},
"measures" : {
"$ref" : "#/$defs/objectField"
},
"pedigrees" : {
"$ref" : "#/$defs/objectField"
},
"phenotypicFeatures" : {
"$ref" : "#/$defs/objectField"
},
"sex" : {
"$ref" : "#/$defs/objectField"
},
"treatments" : {
"$ref" : "#/$defs/objectField"
}
},
"$defs" : {
"objectField" : {
"type" : "object" ,
"additionalProperties" : false ,
"properties" : {
"fields" : {
"oneOf" : [
{
"type" : "string"
},
{
"$ref" : "#/$defs/arrayField"
}
]
},
"dictionary" : {
"type" : "object" ,
"additionalProperties" : {
"type" : "string"
}
},
"selector" : {
"type" : "object" ,
"additionalProperties" : {
"type" : "object"
}
},
"routeOfAdministration" : {
"type" : "object" ,
"additionalProperties" : {
"type" : "string" ,
"enum" : [
"oral" ,
"rectal" ,
"intravenous" ,
"intramuscular" ,
"subcutaneous" ,
"inhalation" ,
"topical" ,
"transdermal" ,
"sublingual" ,
"buccal" ,
"intranasal" ,
"ocular" ,
"otic" ,
"vaginal" ,
"intrathecal" ,
"epidural"
]
}
},
"ontology" : {
"type" : "string" ,
"enum" : [
"ncit" ,
"ohdsi" ,
"cdisc" ,
"omim" ,
"hpo"
]
},
"mapping" : {
"type" : "object" ,
"additionalProperties" : {
"type" : "string"
}
},
"terminology" : {
"type" : "object" ,
"additionalProperties" : {
"type" : "object" ,
"properties" : {
"id" : {
"type" : "string" ,
"pattern" : "^\\w[^:]+:.+$"
},
"label" : {
"type" : "string"
}
},
"required" : [
"id" ,
"label"
],
"additionalProperties" : false
}
},
"assignTermIdFromHeader" : {
"$ref" : "#/$defs/arrayField"
},
"drugDose" : {
"type" : "object" ,
"additionalProperties" : {
"type" : "string"
}
},
"duration" : {
"type" : "object" ,
"additionalProperties" : {
"type" : "string"
}
},
"drugUnit" : {
"type" : "object" ,
"additionalProperties" : {
"type" : "string"
}
},
"durationUnit" : {
"type" : "object" ,
"additionalProperties" : {
"type" : "string"
}
},
"bodySite" : {
"type" : "object" ,
"additionalProperties" : {
"type" : "string"
}
},
"dateOfProcedure" : {
"type" : "object" ,
"additionalProperties" : {
"type" : "string"
}
},
"ageOfOnset" : {
"type" : "object" ,
"additionalProperties" : {
"type" : "string"
}
},
"familyHistory" : {
"type" : "object" ,
"additionalProperties" : {
"type" : "string"
}
},
"unit" : {
"type" : "object" ,
"additionalProperties" : {
"type" : "object" ,
"properties" : {
"label" : {
"type" : "string"
},
"referenceRange" : {
"type" : "object" ,
"properties" : {
"low" : {
"type" : "number"
},
"high" : {
"type" : "number"
}
},
"required" : [
"low" ,
"high"
]
},
"procedureCodeLabel" : {
"$ref" : "#/$defs/stringField"
}
},
"required" : [
"label" ,
"referenceRange"
]
}
}
},
"required" : [
"fields"
]
},
"stringField" : {
"type" : "string"
},
"arrayField" : {
"type" : "array" ,
"items" : {
"type" : "string"
}
}
}
}
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