PhenotypicFeature sb-phenopackets

{S}[B] Status [i]
implemented
Provenance
Used by
Contributors
Source (v1.0.0)

Attributes

Type: object
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)

Properties

Property Type
ageOfOnset https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/Age.json [SRC] [HTML]
ageRangeOfOnset https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/AgeRange.json [SRC] [HTML]
classOfOnset https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/OntologyClass.json [SRC] [HTML]
description string
evidence https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/Evidence.json [SRC] [HTML]
modifiers array of "https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/OntologyClass.json [SRC] [HTML]"
negated boolean
severity https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/OntologyClass.json [SRC] [HTML]
type https://schemablocks.org/schemas/sb-phenopackets/v1.0.0/OntologyClass.json [SRC] [HTML]

ageOfOnset

The age at disease onset. FHIR mapping: Condition.onset

ageOfOnset Value Example
{
   "age" : "P35Y"
}

ageRangeOfOnset

the values of this will come from the HPO onset hierarchy i.e. subclasses of HP:0003674 FHIR mapping: Condition.onset

ageRangeOfOnset Value Example
{
   "start" : {
      "age" : "P35Y"
   }
}

classOfOnset

The values of this will come from the HPO onset hierarchy i.e. subclasses of HP:0003674 FHIR mapping: Condition.onset

classOfOnset Value Example
{
   "id" : "HP:0003596",
   "label" : "Middle age onset"
}

description

Free-text description of the phenotype. Note this is not a acceptable place to document/describe the phenotype - the type and onset etc… fields should be used for this purpose.

description Value Example
"Pancreatic Adenocarcinoma"

evidence

Evidences for how the phenotype was determined.

evidence Value Example
{
   "evidenceCode" : {
      "id" : "add example",
      "label" : "add example"
   },
   "reference" : {
      "description" : "add example",
      "id" : "add example"
   }
}

modifiers

subclasses of HP:0012823 ! Clinical modifier apart from Severity HP:0012824 - Severity

modifiers Value Example
[
   {
      "id" : "HP:0025282",
      "label" : "Dull"
   }
]

negated

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

negated Value Example
"false"

severity

Severity of the condition e.g. subclasses of HP:0012824-Severity or SNOMED:272141005-Severities FHIR mapping: Condition.severity

severity Value Example
{
   "id" : "HP:0012825",
   "label" : "Mild"
}

type

The primary ontology class which describes the phenotype. FHIR mapping: Condition.identifier

type Value Example
{
   "id" : "add example",
   "label" : "Craniosynostosis"
}

PhenotypicFeature Value Example

{
   "ageOfOnset" : {
      "id" : "HP:0003596",
      "label" : "Middle age onset"
   },
   "description" : "add example",
   "evidence" : {
      "evidenceCode" : {
         "id" : "add example",
         "label" : "add example"
      },
      "reference" : {
         "description" : "add example",
         "id" : "add example"
      }
   },
   "modifiers" : [
      {
         "id" : "HP:0025282",
         "label" : "Dull"
      }
   ],
   "negated" : "",
   "severity" : {
      "id" : "HP:0012825",
      "label" : "Mild"
   },
   "type" : {
      "id" : "add example",
      "label" : "add example"
   }
}