Phenopacket Schema Versions Save

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

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"
        }]
      }]
    }

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

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.

Release candidate version for discussion at the next GA4GH Connect meeting

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

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.