Type: object
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

• type: ./timeElement.json

ageOfOnset Value Examples

{
   "age" : {
      "iso8601duration" : "P32Y6M1D"
   },
   "ageGroup" : {
      "id" : "NCIT:C49685",
      "label" : "Adult 18-65 Years Old"
   }
}

{
   "ageRange" : {
      "end" : {
         "iso8601duration" : "P59Y"
      },
      "start" : {
         "iso8601duration" : "P18Y"
      }
   }
}

{
   "age" : {
      "iso8601duration" : "P2M4D"
   }
}

diseaseCode

• type: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json [LINK]

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

diseaseCode Value Examples

{
   "id" : "HP:0004789",
   "label" : "lactose intolerance"
}

{
   "id" : "ICD10CM:E73",
   "label" : "lactose intolerance"
}

{
   "id" : "OMIM:164400",
   "label" : "Spinocerebellar ataxia 1"
}

familyHistory

• type: boolean

Boolean indicating determined or self-reported presence of family history of the disease.

familyHistory Value Example

"1"

notes

• type: string

Unstructured text to describe additional properties of this disease instance.

notes Value Example

"Some free text"

severity

• type: ./commonDefinitions.json#/definitions/SeverityLevel

severity Value Examples

{
   "id" : "HP:0012828",
   "label" : "Severe"
}

{
   "id" : "HP:0012826",
   "label" : "Moderate"
}

stage

• type: https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/framework/json/common/ontologyTerm.json [LINK]

Ontology term from Ontology for General Medical Science (OGMS), e.g. acute onset (OGMS:0000119). Provenance: GA4GH Phenopackets v2 Disease.disease_stage

stage Value Examples

{
   "id" : "OGMS:0000119",
   "label" : "acute onset"
}

{
   "id" : "OGMS:0000117",
   "label" : "asymptomatic"
}

{
   "id" : "OGMS:0000106",
   "label" : "remission"
}