This is no an exhaustive list of changes, but highlights the most important additions and breaking changes.
- Removed genes and variant fields. These should be sent as part of an Interpretation.
- Removed variant field. These should be sent as part of an Interpretation.
- Added a new TimeElement message to wrap all the previous oneof in Individual, Biosample, Disease, PhenotypicFeature
message TimeElement {
oneof element {
GestationalAge gestational_age = 6;
Age age = 1;
AgeRange age_range = 2;
OntologyClass ontology_class = 3;
google.protobuf.Timestamp timestamp = 4;
TimeInterval interval = 5;
}
}
- Added new GestationalAge message for pre-natal individuals and samples
- Replaced oneof age_at_collection with new TimeElement message
- Added new OntologyClass gender field
- Added new VitalStatus field
- Added new message for capturing the vital status of an individual
- Replaced oneof onset with new TimeElement message
- Replaced oneof onset with new TimeElement message
- Added new Measurement message for capturing quantitative, ordinal (e.g., absent/present), or categorical measurements. This element is available as a repeated field in the Phenopacket and Biosample top-level elements.
- Added new MedicalAction to capture medications, procedures, other actions taken for clinical management. This element is available as a repeated field in the Phenopacket.
- Interpretation is now a sub-element of a Phenopacket, rather than an enclosing element. The change allows for better semantics on the Gene and Variant types and their relationship to an Individual or Biosample in the context of a Diagnosis based on a GenomincInterpretation.