{
"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"
}
}
}
}