phenopacket-schema
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phenopackets
Implement GA4GH Pedigree model
@buske
Will require an ethnicity field adding to Individual:
Re-opening given discussion with Pedigree group on 2022-03-03. This field is useful/required for many test ordering systems. The codes used will likely be national-specific codes and not necessarily universally applicable.
Originally posted by @julesjacobsen in https://github.com/phenopackets/phenopacket-schema/issues/231#issuecomment-1058533105
@buske - please add the link to the conceptual model docs when this has been finalised.
Plan is to add org.ga4gh.pedigree.Pedigree and component classes, composed using Phenopacket-schema entities i.e. Individual, OntologyClass.
The GA4GH Pedigree would be incorporated as a oneof in the Family.pedigree field.
- [ ] Implement classes
- [ ] Update Family
- [ ] Test backwards compatibility
- [ ] Update Docs
- [ ] Drink Tea
A note on backward compatibility - if it is not possible for the pedigree to be made a oneof we will have to try another solution.
@julesjacobsen I think this is something we will have to leave for a future version? Should we close?
Hi everyone, sorry to budge in this thread, but I was wondering if you could give more details about the future population building block. I came from https://github.com/phenopackets/phenopacket-schema/issues/231, and I also am interested in having ethnicity part of a phenopacket.
Regardless of what the final implementation is, would it include both ancestry informative markers (Ancestry category [HANCESTRO:0004]) and other less informative markers (in case the former are missing; e.g. National origin [NCIT:C28407] or Ethnic group [EFO:0001799]).
Currently https://github.com/phenopackets/phenopacket-schema/commit/727b245c0ec0df71467344eef7d04cb07b00ae9e
This is external to the phenopacket-schema as it lives in the org.ga4gh.pedigree namespace and imports Phenopacket and OntologyClass . This might change to use the Pedigree model Individual and potentially a Concept (would be identical to OntologyClass, only native to the Pedigree model to reduce depencencies)
@M-casado have you got a use-case and model in mind? If so please continue this in #231
Hi @julesjacobsen, I do not a specific use-case and model in mind. There is a general desire from the users of my archive (EGA) to be able to provide the ethnicity of their probands, and we will try to conform to phenopackets.