Add alliancegenome.org as provider a for all NHGRI MODs

Question

Add alliancegenome.org as provider a for all NHGRI MODs

Closed this issue 7 months ago · 4 comments

For each of

wormbase
flybase
rgd
mgi
zfin
xenbase
sgd

Add an alternative resolver to https://www.alliancegenome.org/

Note: in time some of these MODs may wish to

I am currently discussing a generic resolver, as we want to avoid {wormbase,flybase,...}.{gene,allele,variant,transgene} cross-product explosion pf prefixes

Answer 1 · 2024-06-06T14:18:48.000Z

Thanks @cmungall, we will add alliancegenome.org as a provider for these databases

Answer 2 · 2024-06-06T19:33:01.000Z

Hi @cmungall, after a review of the resources you listed, we found that all of them, except xenbase already use alliancegenome.org as a provider. This means you can resolve e.g., SGD entries via the Bioreigsty as https://bioregistry.io/sgd:S000002493?provider=agr (i.e., by giving the provider=agr parameter to the resolver). So for now, the only action needed is adding a provider for xenbase.

Answer 3 · 2024-06-06T21:14:58.000Z

This part is particularly important:

I am currently discussing a generic resolver, as we want to avoid {wormbase,flybase,...}.{gene,allele,variant,transgene} cross-product explosion pf prefixes

Unfortunately the current resolver assumes everything is a gene. Try this

https://bioregistry.io/wb:WBVar00241923?provider=agr

"Page Not Found"

Although genes are the most important, the Alliance will ultimately have many different kinds of entities

I'm hoping bioregistry doesn't inherit the antipattern from identifiers.org where resources were assumed to have only one type, and then new types added ad-hoc, following the <DB>.<TYPE> pattern, with the exception of the main type being <DB>. Meanwhile, a large section of the community use <DB>: as the prefix for all types.