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biopragmatics / bioregistry

📮 An integrative registry of biological databases, ontologies, and nomenclatures.
https://bioregistry.io
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Improve incomplete records from RRID #954

Open cthoyt opened 10 months ago

cthoyt commented 10 months ago

In #952, we aligned the RRID resources with the Bioregistry. However, there are a number of resources referenced in RRID that didn't align to existing Bioregistry prefixes, nor could they be curated as new ones. I've included that table here:

https://github.com/biopragmatics/bioregistry/blob/283961b5450a947494bced680f4ce9b1b167f919/src/bioregistry/align/rrid.py#L15-L30

The question is: is there still a way that RRID incorporates information from these resources? For most of them, I could not actually find any information about the identifier resource. What do you think @bandrow? Is there a way to get example local unique identifiers for these resources that are pre-indexed in RRID? That might be a way forward.

bandrow commented 10 months ago

All of these are animal stock centers so they are under the organism RRID category:

  1. Go to https://scicrunch.org/resources/data/source/nlx_154697-1/search?q=xep&l=xep
  2. grab first result is from xenopus express, and the RRID is RRID:XEP_Xep
  3. can always check https://n2t.net/RRID:XEP_Xep.json = success to see if valid RRID:XEP_Xep RRID:CWRU_CFC RRID:XGSC_SR RRID:SSCLBR_Cdk8 - yes the resource is currently dead, we will need to redirect to RGD shortly; RRID:EXRC_0216 RRID:IMSR_CARD:1153 RRID:IMSR_CMMR:516C10 RRID:IMSR_CRL:023 RRID:IMSR_GPT:T057702 RRID:IMSR_HAR:2115 RRID:IMSR_NIG:186 RRID:IMSR_TIGM:IST14962C7

The place where this will fail is IMSR (as you say this is a pan organization so it contains no specific RRIDs, it houses a bunch of mouse repository data)

I need to figure out what the heck IMSR_NM-KI is that breaks all rules. I will try to track this down

bandrow commented 10 months ago

I see what happened, the curator captured an extra parameter in the RRID:IMSR_NM-KI resource, it should be RRID:IMSR_NM example: RRID:IMSR_NM-NSG-001

-thanks for catching this one, they broke the rules on IDs at this repository, but we didn't catch it.