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biopragmatics / bioregistry

đź“® An integrative registry of biological databases, ontologies, and nomenclatures.
https://bioregistry.io
MIT License
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Merge resource GlyGen into GlyTouCan #1084

Open katewarner opened 3 months ago

katewarner commented 3 months ago

Redundant Prefix

glygen

Target Prefix

glytoucan

Explanation

The local unique identifier in the GlyGen prefix is actually a GlyTouCan ID, as we use these IDs to identify Glycans in GlyGen.

Contributor ORCID

0000-0001-8705-181X

bgyori commented 2 months ago

Hi @katewarner, I think this makes sense. Interestingly, two other registries, Fairsharing, and Integbio also have separate entries for GlyGen and GlyToucan. In any case, what we could do is, keep the glytoucan prefix, but add glygen as a synonym prefix, and also list GlyGen as a "provider" for GlyToucan IDs.

matentzn commented 2 months ago

From the little bit of information in this issue the complete solution comes down to the question of whether the org behind https://glygen.org/ (@jeet-vora) agrees with the assertion that the local id corresponds to a GlyTouCan ID. Right now, both glytoucan and glygen are registered as separate “semantic spaces” covering the same exact local ID space (as far as I can quickly see from the regex rules in both records):

https://bioregistry.io/registry/glygen https://bioregistry.io/registry/glytoucan

If @jeet-vora agrees that the local ids are in fact all glytoucan ids IMO the course of action should be to:

  1. Remove the glygen record entirely
  2. Add the glygen prefix as a prefix synonym to the glytoucan record (as @bgyori suggests)
  3. Add glygen.org as an alternative resolver (uri_prefix_synonym)
  4. While you are at it, add a point of contact to the glytoucan record
bgyori commented 2 months ago

Thanks @matentzn, the PR I opened here https://github.com/biopragmatics/bioregistry/pull/1109 implements what you are suggesting.