biopragmatics / bioregistry

📮 An integrative registry of biological databases, ontologies, and nomenclatures.
https://bioregistry.io
MIT License
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Merge glygen into glytoucan #1109

Closed bgyori closed 1 month ago

bgyori commented 5 months ago

This PR merges glygen into glytoucan while preserving it as a synonym and as a provider for glytoucan IDs. Some issues with this: useful metadata about GlyGen gets lost, for instance its mapping to FairSharing and Integbio, and metadata on a resolver for UniProt IDs on GlyGen.

Fixes #1084

codecov[bot] commented 5 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 43.98%. Comparing base (6092b57) to head (2aeaba5). Report is 138 commits behind head on main.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #1109 +/- ## ======================================= Coverage 43.98% 43.98% ======================================= Files 123 123 Lines 8166 8166 Branches 1900 1900 ======================================= Hits 3592 3592 Misses 4369 4369 Partials 205 205 ```

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bgyori commented 4 months ago

Given that the Bioregistry primarily aims to curate identifier resources, and from that perspective, GlyGen really is just a provider, I think these changes make sense. The metadata (i.e., publications, maintainer, etc.) associated with the GlyGen entry is useful but not strictly from a prefix / identifier pattern / resolver URL perspective which again is the main focus here.

bgyori commented 4 months ago

Hello @jeet-vora, do you have any thoughts on this change?

bgyori commented 1 month ago

Just noticed this is still open, @jeet-vora do you have any comments on this?

jeet-vora commented 1 month ago

@bgyori Sorry missed this.

I would keep GlyTouCan and GlyGen as separate entries. GlyTouCan is a repository for glycans and provides IDs for Them. GlyGen is a knowledgebase that provides information about glycans by using the standard GlyTouCan IDs to represent them. GlyGen also has information about genes and proteins that GlyTouCan does not have. GlyGen does not assign glycan IDs.

Again the above suggestion is based on what I know so far. I my suggestion does not make sense or resolve the issue I might have to dig deep into the communication and the information while I was gone.

bgyori commented 1 month ago

I think perhaps our use of the word "merging" is a bit misleading. What happens in this PR is that we keep glytoucan as the prefix curared in Bioregistry for a namespace of identifiers while curating gylgen as a provider for those identifiers. This, I think, captures what you wrote above.

jeet-vora commented 1 month ago

I see. Thanks Please go ahead as previously planned