Update HUGO Gene Nomenclature Committee

[KrishnaTO]

Prefix

hgnc

Explanation

HGNC has a better built owl file available on their site

Direct link: https://storage.googleapis.com/public-download-files/hgnc/owl/owl/hgnc.owl

Note that the superclasses are better defined in this version, courtesy of Scibite.

Contributor ORCID

0000-0002-2627-0696

[cthoyt]

@KrishnaTO can you further qualify what you mean by "better"?

you might also want to take a look at https://cthoyt.com/2025/10/14/databases-as-ontologies-2-hgnc.html, which explains the design choices in my HGNC ontologization

[KrishnaTO]

It's not a matter of ontology design but formatting (honestly couldn't even compare design via Protege).

Opening the currently linked owl file in protege (and running through ODK new pipeline), there is a long list of broken classes. If you can fix those, happy to use this version.

[cthoyt]

We're not going to change the default link from the Bioregistry, but here's what I can offer:

1. I improved the PyOBO export in:
   • Improve HGNC export pyobo#486 to better incorporate HGNC gene families.
   • Add parents for implicitly declared classes pyobo#488 to better group implicitly declared classes
2. I updated the ontology links in Bioregistry to explicitly point to the OBO-DB-Ingest PURLs, so the OLS artifacts' versioned IRIs don't leak through in Add ontology artifacts from OBO-DB-Ingest #1812
3. I updated the OBO DB Ingest data with the new improvements in Add grouping classes for implicitly declared obo-db-ingest#30

[KrishnaTO]

I understand, thanks for considering the issue and your work on this.