Exposure

This element is intended to be used as a component of the Phenopacket message.

repeated org.phenopackets.schema.v1.core.Exposure exposures = 11;

This represents a list of environmental exposures. The resources using these fields should define what this represents in their context.

Data model

Definition of the Exposure element
Field Type Status Description
description string optional Free-text description of the exposure.
type OntologyClass required The primary ontology class which describes the exposure.
negated bool optional Flag to indicate whether the exposure occurred or not
route OntologyClass optional Mechanism of the exposure
modifiers OntologyClass (repeated) optional Characteristics of the exposure
occurrence TimeElement optional When the exposure occurred
evidence Evidence (repeated) required Evidences for how the exposure was determined.

Example

{
  "description": "accidental arsenic ingestion from a herbal medicine product",
  "type":
      {
          "id": "ECTO:9000032",
          "label": "arsenic atom exposure"
      },
  "route":
      {
          "id": "NCIT:C28229",
          "label": "Ingestion"
      },
  "occurrence":
      {
          "timestamp": "2018-03-01T00:00:00Z"
      },
  "evidence":
       {
          "id": "ECO:0006154",
          "label": "self-reported patient statement evidence"
      }
}

description

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

type

The primary ontology class which describes the exposure (See OntologyClass).

Terms from the Environment Exposure Ontology (ECTO) can be used.

negated

Flag to indicate whether the exposure occurred or not. Default is ‘false’, in other words the exposure has occurred. Therefore it is only required in cases to indicate that the exposure was deemed _not_ to have happened. 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 exposure!

route

Mechanism of the exposure. Ontology terms from the NCIT can be used for this purpose.

modifiers

Ontology class describing the characteristics of the exposure.

occurrence

When the exposure occurred.

evidence

Evidences for how the exposure was determined.