8000 Fix curie presenation and linkout by kkaris · Pull Request #154 · gyorilab/gilda · GitHub
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Fix curie presenation and linkout #154

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Fix curie presenation and linkout #154

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@kkaris kkaris commented May 7, 2025

This PR updates the URL generation and curie presentation:

  • Generated URLs are now pointing to bioregistry.io rather than identifiers.org.
  • Curies are now all lowercase for the namespace.

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bgyori commented May 12, 2025

Thanks @kkaris this is great. Two more things:

  • Some tests that use CURIEs still need to be fixed
  • Please do a review of where, if at all, Gilda-produced CURIEs are used downstream (in INDRA, various Biopragmatics packages, etc.) and check if the change in CURIE style will break something. Alternatively, we can keep the CURIEs as is and just update the base URL in this PR.

@kkaris kkaris force-pushed the fix-curie-presenation branch from e49bbb4 to 2899f5f Compare May 19, 2025 20:51
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kkaris commented May 19, 2025 •
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Tests are fixed and I opted to restore the original functions get_identifiers_curie and get_identifiers_url, but add in warnings that these functions are deprecated in favor of get_curie and get_url, respectively.

For the method Term.get_curie, it now uses the newer get_curie instead of get_identifiers_curie. In practice, the only thing this does is to return all curies with lower case database names.

I also went over most of the dependents in the dependency graph for Gilda, including our packages, to see if anyone might rely on Term.get_curie in a way that would be affected by this PR and I could only find one example so far that I've taken care of already.

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