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monarch-initiative / monarch-gene-mapping

Code for mapping source namespaces to preffered namespacing
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Change wormbase mapping to `wormbase:` #38

Open matentzn opened 8 months ago

matentzn commented 8 months ago

We are using the ideosyncractic WB.

Bioregistry suggests wormbase: for the genes, which I think is fair. Can we change that? Basically, this will make the custom prefix map redundant.

https://bioregistry.io/registry/wormbase

monicacecilia commented 7 months ago

Dear @glass-ships, could I kindly ask if you could please take a look at this issue and assess feasibility? Let me know if you feel comfortable tackling this. Thank you!

glass-ships commented 7 months ago

Hmmm, would this basically entail changing the prefix from WB to wormbase in monarch ingest?

matentzn commented 7 months ago

@glass-ships essentially yes, but you would have to do this carefully in consultation with Kevin as you may have some "baked in assumptions" somewhere at UI or ETL level about which prefixes you expect.

kevinschaper commented 7 months ago

I'm not convinced that bioregistry is right here. WB: is how Wormbase submits their data up to the Alliance, and what is displayed on Alliance pages (which Wormbase contributes to the creation of) that link back to wormbase.org. What do you think @sierra-moxon?

kevinschaper commented 7 months ago

I see NCBI and Panther using WormBase and the GAF files have WB

matentzn commented 6 months ago

I am adding WB at least to bioregistry: https://github.com/biopragmatics/bioregistry/pull/1042