biopragmatics / bioregistry

📮 An integrative registry of biological databases, ontologies, and nomenclatures.
https://bioregistry.io
MIT License
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Add upper- and lowercase prefix synonyms #969

Open cthoyt opened 10 months ago

cthoyt commented 10 months ago

Closes #935

This PR automatically adds both the upper- and lowercase variants of all prefix synonyms for each record. This makes it much more simple to create comprehensive EPMs (instead of having to refer on programmatic logic for matching)

Depends on

codecov[bot] commented 10 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Comparison is base (488c954) 40.57% compared to head (6fdc65f) 40.90%. Report is 16 commits behind head on main.

:exclamation: Current head 6fdc65f differs from pull request most recent head c650c44. Consider uploading reports for the commit c650c44 to get more accurate results

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #969 +/- ## ========================================== + Coverage 40.57% 40.90% +0.32% ========================================== Files 148 138 -10 Lines 8244 7916 -328 Branches 1910 1849 -61 ========================================== - Hits 3345 3238 -107 + Misses 4690 4475 -215 + Partials 209 203 -6 ```

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cthoyt commented 4 months ago

The current issue why this isn't working is in the OBO context, the OBO synonyms are prioritized, which gives the Geographical Entity ontology the GEO prefix, but doesn't unprioritize the geo prefix for Gene Expression Omnibus since this logic is case-sensitive