PhenotypicFeature

This element is intended to be used to describe a phenotype that characterizes the subject of the Phenopacket. For medical use cases the subject will generally be a patient or a proband of a study, and the phenotypes will be abnormalities described by an ontology such as the Human Phenotype Ontology. The word phenotype is used with many different meanings including disease entity, but in this context we mean An individual phenotypic feature, observed as either present or absent (negated), with possible onset, modifiers and frequency.

Data model

Field Type Status Description    
description string optional human-readable verbiage NOT for structured text    
type OntologyClass required term denoting the phenotypic feature    
negated boolean optional defaults to false    
severity OntologyClass optional description of the severity of the feature described in type representing HP:0012824    
modifier list of OntologyClass optional representing one or more terms from HP:0012823    
onset OntologyClass optional Age at which the features was first observed e.g. HP:0011462
evidence Evidence recommended the evidence for an assertion of the observation of a type    

Example

{
    "type": {
      "id": "HP:0000520",
      "label": "Proptosis"
    },
    "severity": {
        id": "HP:0012825",
        "label": "Mild"
    }
    "classOfOnset": {
      "id": "HP:0003577",
      "label": "Congenital onset"
    }
}

description

This element represents a free-text description of the phenotype. It should not be used as the primary means of describing the phenotype, but can be used to supplement the record if ontology terms are not sufficiently able to capture all the nuances. In general, the type and onset etc… fields should be used for this purpose, and this field is a last resort.

type

The element represents the primary ontology class which describes the phenotype. For example Craniosynostosis (HP:0001363).

negated

This element is a flag to indicate whether the phenotype was observed or not. The 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.

severity

This element is an ontology class that describes the severity of the condition e.g. subclasses of Severity (HP:0012824) or SNOMED:272141005-Severities

modifier

This element is a list of ontology class elements that can be empty or contain one or more ontology terms that are intended to provide more expressive or precise descriptions of a phenotypic feature, including attributes such as positionality and external factors that tend to trigger or ameliorate the feature. Terms can be taken from the hierarchy of Clinical modifier in the HPO (noting that severity should be coded in the severity element).

onset

This element can be used to describe the age at which a phenotypic feature was first noticed or diagnosed. For many medical use cases, either the Age sub-element or an ontology class (e.g., from the HPO Onset (HP:0003674) terms) will be used.

evidence

This element is recommended and contain one or more Evidence elements that specify how the phenotype was determined.