Phenotype

From Phenopacket schema

Status: proposed

Provenance

Used by

Authors

Schema source: YAML file

Properties of the Phenotype class

Property Type Format Description
description string Free-text description of the phenotype. Note this is not a acceptable place to document/describe the phenotype the type and onset etc... Other fields should be used for this purpose.
evidence array ./Ontology_term Evidences for how the phenotype was determined
negated boolean Flag to indicate whether the phenotype was observed or not. Default is 'false', in other words the phenotype was observed. It is only required in cases to indicate that the phenotype was looked for, but __not__ observed.
onset ./Age The age of onset, as Age object. In the Phenopacket implementation, alternatives to the "Age" class may be used to describe "onset".
severity ./Ontology_term Severity of the condition e.g. subclasses of HP:0012824-Severity or SNOMED:272141005-Severities. FHIR mapping: Condition.severity
type ./Ontology_term The ontology term as Ontology_term. The primary ontology class which describes the phenotype.

Description

An individual phenotypic feature, observed as either present or absent (negated), with possible onset, modifiers and frequency. FHIR mapping: Condition (https://www.hl7.org/fhir/condition.html) or Observation (https://www.hl7.org/fhir/observation.html)

Examples

{
   "description" : "DUO:0000004",
   "evidence" : [
      {
         "id" : "",
         "label" : ""
      }
   ],
   "negated" : "",
   "severity" : {
      "id" : "HP:0012825",
      "label" : "Mild"
   },
   "type" : {
      "id" : "ncit:C8294",
      "label" : "Pancreatic Adenocarcinoma"
   }
}

Notes and examples on the Phenotype properties

description
'description' : "Pancreatic Adenocarcinoma"
evidence
'evidence' : [
  {
    'id' => '',
    'label' => ''
  }
]
negated
'negated' : ""
onset
'onset' : {
  'age' => 'P12Y',
  'age_class' => {
                   'id' => 'HP:0003621',
                   'label' => 'Juvenile onset'
                 }
}
severity
'severity' : {
  'id' => 'HP:0012825',
  'label' => 'Mild'
}
type
'type' : {
  'id' => 'ncit:C8294',
  'label' => 'Pancreatic Adenocarcinoma'
}
Edit on Github...