disease.json

{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "description": "Diseases diagnosed e.g. to an individual, defined by diseaseID, age of onset, stage, level of severity, outcome and the presence of family history. Similarities to GA4GH Phenopackets v2 `Disease`",
    "properties": {
        "ageOfOnset": {
            "$ref": "./timeElement.json",
            "examples": [
                {
                    "id": "NCIT:C49685",
                    "label": "Adult 18-65 Years Old"
                },
                {
                    "iso8601duration": "P32Y6M1D"
                },
                {
                    "end": {
                        "iso8601duration": "P59Y"
                    },
                    "start": {
                        "iso8601duration": "P18Y"
                    }
                },
                {
                    "iso8601duration": "P2M4D"
                }
            ]
        },
        "diseaseCode": {
            "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
            "description": "Disease identifier. Value from disease ontologies such as HPO, OMIM, Orphanet, MONDO, e.g. lactose intolerance (HP:0004789, ICD10CM:E73). Provenance: GA4GH Phenopackets v2 `Disease.term`",
            "examples": [
                {
                    "id": "HP:0004789",
                    "label": "lactose intolerance"
                },
                {
                    "id": "ICD10CM:E73",
                    "label": "lactose intolerance"
                },
                {
                    "id": "OMIM:164400",
                    "label": "Spinocerebellar ataxia 1"
                }
            ]
        },
        "familyHistory": {
            "description": "Boolean indicating determined or self-reported presence of family history of the disease.",
            "examples": [
                true
            ],
            "type": "boolean"
        },
        "notes": {
            "description": "Unstructured text to describe additional properties of this disease instance.",
            "examples": [
                "Some free text"
            ],
            "type": "string"
        },
        "severity": {
            "$ref": "./commonDefinitions.json#/$defs/SeverityLevel",
            "examples": [
                {
                    "id": "HP:0012828",
                    "label": "Severe"
                },
                {
                    "id": "HP:0012826",
                    "label": "Moderate"
                }
            ]
        },
        "stage": {
            "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json",
            "description": "Ontology term from Ontology for General Medical Science (OGMS), e.g. acute onset (OGMS:0000119). Provenance: GA4GH Phenopackets v2 `Disease.disease_stage`",
            "examples": [
                {
                    "id": "OGMS:0000119",
                    "label": "acute onset"
                },
                {
                    "id": "OGMS:0000117",
                    "label": "asymptomatic"
                },
                {
                    "id": "OGMS:0000106",
                    "label": "remission"
                }
            ]
        }
    },
    "required": [
        "diseaseCode"
    ],
    "title": "Disease",
    "type": "object"
}