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Published 20 hours ago • verified publisher icon vaccineontology

Convert mappings to SSSOM files

Open cthoyt opened this issue 5 months ago • 3 comments

This PR adds a script that converted the original mapping CSV files into standardized, self-contained SSSOM (Simple Standard for Sharing Ontological Mappings).

There are still a few TODOs/questions to finish this:

  • [x] what's the USDA namespace? We can register this in the bioregistry too. (https://github.com/biopragmatics/bioregistry/pull/1562)
  • [ ] How were these mappings produced? SSSOM can capture more information about this
  • [x] Add mapping set IDs, titles, and other SSSOM-metadata (done in 54943a4)
  • [ ] What is going on in the RxNorm extensions file? The IDs have OMOP in their prefixes.

cthoyt avatar May 06 '25 11:05 cthoyt