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PavlidisLab / TGEMO

The Gemma Ontology
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Only copy over the direct superclass of our terms from other ontologies #20

Open arteymix opened 9 months ago

arteymix commented 9 months ago

This makes it much easier to work with the ontology file and in principle shouldn't affect our ability to perform ontology inference.

I have to check first if the inference with Gemma still works properly as we would be lacking the full set of super/sub-class hierarchy and part of/has part relations.

arteymix commented 9 months ago

Yes, this is about performance for both Gemma but also QoL for curators that have to wait 5 minutes for Protégé to load right now.

arteymix commented 9 months ago

I've addressed the issue of inference across ontologies in https://github.com/PavlidisLab/Gemma/commit/4300e7759a6e5191f095ba0a048e3492ef36fade, and I already went ahead with disabling import for TGEMO in tests to speed them up. This will be in the 1.31, so I'll wait until it's out before merging.