--------------
This is no an exhaustive list of changes, but highlights the most important additions and breaking changes.
Phenopacket
~~~~~~~~~~~
- Removed `genes` and `variant` fields. These should be sent as part of an `Interpretation`.
Biosample
~~~~~~~~~~~
- Removed `variant` field. These should be sent as part of an `Interpretation`.
TimeElement
~~~~~~~~~~~
- Added a new `TimeElement` message to wrap all the previous `oneof` in `Individual`, `Biosample`, `Disease`, `PhenotypicFeature`
.. code-block::
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;
}
}
GestationalAge
~~~~~~~~~~~~~~
- Added new `GestationalAge` message for pre-natal individuals and samples
Individual
~~~~~~~~~~
- Replaced oneof `age_at_collection` with new `TimeElement` message
- Added new `OntologyClass` `gender` field
- Added new `VitalStatus` field
VitalStatus
~~~~~~~~~~~
- Added new message for capturing the vital status of an individual
PhenotypicFeature
~~~~~~~~~~~~~~~~~
- Replaced oneof `onset` with new `TimeElement` message
Disease
~~~~~~~~~~~~~~~~~
- Replaced oneof `onset` with new `TimeElement` message
Measurement
~~~~~~~~~~~
- 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.
MedicalAction
~~~~~~~~~~~~~
- 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
~~~~~~~~~~~~~~
- `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`.