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monarch-initiative / mondo-ingest

Coordinating the mondo-ingest with external sources
https://monarch-initiative.github.io/mondo-ingest/
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Bug: `omim.ps` #576

Open joeflack4 opened 5 months ago

joeflack4 commented 5 months ago

Overview

Sometimes omim.sssom.tsv has omim.ps prefixes instead of OMIMPS.

Background

This has to do with recent changes in BioRegistry (https://bioregistry.io/registry/omim.ps).

matentzn commented 5 months ago

I added something to the global context,

but it should work by fixing the external metadata map provided in

https://github.com/monarch-initiative/mondo-ingest/blob/5e6f26a827ed54c90eb7bef525a440b7e274a2dd/src/ontology/mondo-ingest.Makefile#L201

make sure the prefix and prefix uri listed in the external metadata aligns with what is in omim.owl.

joeflack4 commented 5 months ago

@matentzn Can you elaborate a bit more?

It sounds like you updated a context JSON file in sssom-py, so first I will need to make sure that the package is upgraded.

I checked metadata/omim.metadata.sssom.yml, and in its curie_map, it has: OMIM: https://omim.org/entry/

Surprisingly, it doesn't have an entry for OMIMPS! It seems to me like it should have an entry for that...

Meanwhile, by omim.owl, I assume you mean the one coming from the omim repository? Or maybe mondo-ingest components/omim.owl? These don't use OMIM/OMIMPS prefixes; just the URIs, which haven't changed. The URI prefix is still: https://omim.org/entry/, which is consistent with this metadata file.

What should I do / check next?

matentzn commented 5 months ago

It sounds like you updated a context JSON file in sssom-py, so first I will need to make sure that the package is upgraded.

It will take a long time till that change trickles through. An it is not needed:

Surprisingly, it doesn't have an entry for OMIMPS! It seems to me like it should have an entry for that...

Yes! Just add that there!

These don't use OMIM/OMIMPS prefixes; just the URIs, which haven't changed. The URI prefix is still: https://omim.org/entry/, which is consistent with this metadata file.

Check that the PS URI (!) prefix is mapped correctly in that metadata file to the OMIMPS prefix. I think this will work!

joeflack4 commented 5 months ago

Ok, I see. This is lower priority, I might do this next week.

So after that change, I assume I just need to re-run whatever goals are necessary to regenerate whichever file(s) had omim.ps, and see if it's fixed.