Release 2.0.0

Release v2.0 of the GA4GH Phenopacket schema as approved 2021-06-04

Release 1.0.0

Update README for version 1.0.0

Final release candidate

This is the final release candidate, bar any unforeseen blockers. It is expected that the model will remain unchanged for the final release.

The final breaking change was to the Disease message where tumorStage was changed to tnmFinding and a new diseaseStage field has been added (issue #188). Please see the docs for the updated specification and example.

In the RC3 version Disease was represented like this:

{
      "diseases": [{
        "term": {
          "id": "NCIT:C39853",
          "label": "Infiltrating Urothelial Carcinoma"
        },
        "tumorStage": [{
          "id": "NCIT:C48766",
          "label": "pT2b Stage Finding"
        }, {
          "id": "NCIT:C48750",
          "label": "pN2 Stage Finding"
        }]
      }]
    }

Now in RC4 tumorStage has changed to tnmFinding

{
      "diseases": [{
        "term": {
          "id": "NCIT:C39853",
          "label": "Infiltrating Urothelial Carcinoma"
        },
        "diseaseStage": [{
          "id": "NCIT:C27971",
          "label": "Stage IV"
        }],
        "tnmFinding": [{
          "id": "NCIT:C48766",
          "label": "pT2b Stage Finding"
        }, {
          "id": "NCIT:C48750",
          "label": "pN2 Stage Finding"
        }, {
          "id": "NCIT:C48700",
          "label": "M1 Stage Finding"
        }]
      }]
    }

Post-GA4GH Product Review Committee release

This release candidate has incorporated the changes from the PRC (Product Review Committee) meetings.

Major changes:
We have removed the File type and replaced it the HtsFile
Gene now requires the use of the official organism nomenclature committee identifier, but allows alternative identifiers. See #199
Individual now has optional additional identifiers. See #200
A new Update message has been added to MetaData to allow for more information about who and what happened when an update was made. See #190
The Biosample.tumor_stage was incorrectly modelled and has been moved to Disease.tumor_stage. See #188

GA4GH release candidate for the Product Review Committee

With this release we have removed the MurineAllele and Variant.background as it wasn't fully fit for purpose. There is also a new Interpretation element for use with reporting interpretations based on analysis of data reported in the phenopacket.

GA4GH Connect release candidate

Release candidate version for discussion at the next GA4GH Connect meeting

v0.1.0: Add Disease onset field

Please note that this release is not compatible with the 0.0.7 release. There are limited changes which may or may not impact your usage. Notable changes are as follows:

Changed primary Individual name from patient to subject in phenopackets.proto
Added new HtsFile message for capturing High-Throughput Sequencing file information to base.proto
Replaced File vcf and GenomeAssembly in PhenoPacket with repeated HtsFile hts_files in phenopackets.proto
Added Resource.iri_prefix in base.proto
Added Disease.onset field in base.proto

Added new PhenoPacketFormat utility class for converting to/from JSON and YAML

For your eyes only...

This is a pre-1.0.0 release and may be subject to change, although the initial period of massive change should be over and therefore this should be considered usable.