Implement GA4GH Pedigree model

[julesjacobsen]

@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 #231 (comment)

[julesjacobsen]

@buske - please add the link to the conceptual model docs when this has been finalised.

[julesjacobsen]

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.

[julesjacobsen]

• 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.

[pnrobinson]

@julesjacobsen I think this is something we will have to leave for a future version? Should we close?

[M-casado]

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 #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]).

[julesjacobsen]

Currently 727b245

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)

[julesjacobsen]

@M-casado have you got a use-case and model in mind? If so please continue this in #231

[M-casado]

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.

[cmungall]

What's the status of this?

[julesjacobsen]

This is work in progress and taking lead from the GA4GH-Pedigree working group.