phenopacket-schema
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phenopackets
Repository for the GA4GH phenopacket schema
I'm trying protobuf-jsonschema, it used to work on v1 but it's having issues with paths.. I don't know if protobuf-jsonschema isn't following the spec or it's some configuration I'm trying...
While developing https://github.com/phenopackets/phenopacket-validator, I am noticing that several of the examples in this repository are not valid. For instance, the AML example shows this error ``` $.metaData.resources[0].iriPrefix: is missing but...
- [ ] Test locally if the python PR is still valid in v2 - [ ] Make changes as necessary - [ ] Deploy to pypi/conda - test env...
https://github.com/phenopackets/phenopacket-schema/blob/v2/docs/requirements.rst
e.g. https://phenopacket-schema.readthedocs.io/en/v2/fhir.html links to http://phenopackets.org/core-ig/master/ which is 404 Should be http://phenopackets.org/core-ig/ There may be other broken links
@mbaudis @pnrobinson The PRC required a more extensible replacement for `HtsFile`. The comments and responses quoted below are from the PRC review. PRC initial comment: > Even among “hts_files” there...
The `Disease` object references `OntologyClass` for [ICD-O values](https://github.com/phenopackets/phenopacket-schema/blob/d3c75d358d99c8d479a2d433a9ea39cf71ad592d/src/main/proto/phenopackets/schema/v2/core/disease.proto#L47) used for `primary_site` annotations. Which ICD-O ontology implementation does this refer to? While the codes themselves are well defined/known, It is no...
The v2 documentation provides different options for TNM findings: * `clinical_tnm_finding` in `Disease`, with the description "child terms of NCIT:C48232 (Cancer TNM Finding)" and examples [in the documentation](https://phenopacket-schema.readthedocs.io/en/latest/cancer-example.html#diseases) (but partially...
This might have been an oversight ICGC uses these items -- I think that you could calculate the total dose with either. We might need to ask. radiation_therapy_fractions Indicate the...
