Type: object
Description: Used to describe a phenotype that characterizes the subject or biosample.

Properties

evidence

• type: ./evidence.json

The evidence for an assertion of the observation of a type. RECOMMENDED.

excluded

• type: boolean

(from Phenopackets v.2) Flag to indicate whether the disease was observed or not. Default is ‘false’, in other words the disease was observed. Therefore it is only required in cases to indicate that the disease was looked for, but found to be absent. More formally, this modifier indicates the logical negation of the OntologyClass used in the ‘featureType’ field. CAUTION It is imperative to check this field for correct interpretation of the disease!

featureType

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

Term denoting the phenotypic feature, preferably using a value from Human Phenotype Ontology (HPO)

featureType Value Examples

{
   "id" : "HP:0000002",
   "label" : "Abnormality of body height"
}

{
   "id" : "HP:0002006",
   "label" : "Facial cleft"
}

{
   "id" : "HP:0012469",
   "label" : "Infantile spasms"
}

modifiers

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

For instance one or more terms from HPO Clinical Modifier (HP:0012823). This subontology is designed to provide terms to characterize and specify the phenotypic abnormalities defined in the Phenotypic abnormality subontology, with respect to severity, laterality, age of onset, and other aspects. [ HPO:probinson ]

modifiers Value Examples

{
   "id" : "HP:0032500",
   "label" : "Exacerbated by tobacco use"
}

{
   "id" : "HP:4000053",
   "label" : "Displaced fracture"
}

notes

• type: string

Unstructured text to describe additional properties of this phenotypic feature.

notes Value Example

"Some free text"

onset

• type: ./timeElement.json

Age or time at which the feature was first observed.

resolution

• type: ./timeElement.json

Age or time at which the feature resolved or abated.

severity

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

severity Value Examples

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

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