Improve HGNC export - #486
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Motivated by biopragmatics/bioregistry#1811, follow-up to #486. This PR adds a function that can be used to search all terms in an ontology, identify external references that weren't explicitly declared as a class in the ontology, and add a declaration. All terms declared this way get put under an ontology-wide _ad hoc_ grouping term, which in turn has children corresponding to each prefix for which undeclared classes were found. For example, in HGNC, the ontology-wide grouping term is http://purl.obolibrary.org/obo/hgnc#aux, under which are terms like http://purl.obolibrary.org/obo/hgnc#aux-ec (fo Here's how it looks for HGNC: <img width="1019" height="961" alt="Screenshot 2026-02-22 at 17 30 02" src="https://github.com/user-attachments/assets/77592273-eb81-45ca-bd73-951ddb471d1c" /> There are a few caveats to this approach: 1. Axiom injection (馃し) 2. Doesn't get nice metadata like labels 3. Weird looking labels because there are no labels (will be improved with protegeproject/protege#1322)
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Motivated by biopragmatics/bioregistry#1811
This PR does the following:
This does not solve the more generic issue that PyOBO exports OFN and OWL products using IRIs instead of stringified CURIEs in annotations. This means that if the IRI isn't defined, then Protege tries its best to guess a label, and which pollutes the class list when exploring.