VP data addition: add the number of litvar citations and other data for pgx precuration

ClinGen / gene-and-variant-curation-tools

ClinGen's gene and variant curation interfaces (GCI & VCI). Developed by Stanford ClinGen team.

https://curation.clinicalgenome.org/

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VP data addition: add the number of litvar citations and other data for pgx precuration #285

Open cgpreston opened 1 year ago

cgpreston commented 1 year ago

Requested by the PharmGKB group:

Priority 1: Add the number of LitVar citations in as data and a filter for the VP. Lower priority: CPIC allele function, PharmGKB CA levels.

wrightmw commented 1 year ago

I think the VP is referenced via CA IDs currently.... whereas a quick look at LitVar suggests rsIDs... so would we need to lookup rsIDs in the CAR to be able to return LitVar data?

cgpreston commented 1 year ago

@wrightmw, we'd have to explore if there is a useful way to do LitVar data searches via a truly unique (CAR or ClinVar) ID, otherwise I think the LDH would need to pull these values via the rs ID and we could put a note in the VP filter mentioning that is the value being used. The CAR does annotate variants by their rsID.