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information-artifact-ontology / ontology-metadata

OBO Metadata Ontology
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Why are SSSOM mappings not included in OMO build/release? #130

Closed cthoyt closed 1 year ago

cthoyt commented 1 year ago

Originally stated in https://github.com/information-artifact-ontology/ontology-metadata/commit/83e0301da8b2d924b60eed39305e3f15a068891f#commitcomment-113398830:

it doesn't look like the mappings from https://github.com/information-artifact-ontology/ontology-metadata/blob/master/src/ontology/components/omo-to-external.tsv got pulled in to this release

matentzn commented 1 year ago

This repo is not set up for sssom inclusion yet.. Does the absence of those mappings in omo.owl cause a problem for you now? Blocker I mean?

cthoyt commented 1 year ago

it's not a blocker since I currently maintain these mappings in https://github.com/biopragmatics/bioontologies/blob/main/src/bioontologies/upgrade/data.tsv, but ideally i want to do this curation in OMO instead of maintaining it as a 3rd party resource

matentzn commented 1 year ago

Why isnt it sufficient to supply the sssom files, versioned, in the repo? Is it necessary to add those mappings into the OMO vocab? Remember that if we add them, we add some pretty bad signature to the small OMO ontology, which we really need to keep small and nimble.

cthoyt commented 1 year ago

That's a good point, which is also valid. I thought the idea was more generally integrate the SSSOM files in the ontologies on build (and just to simplify/streamline curation using the format). If you weren't planning on doing that, it's fine for me

matentzn commented 1 year ago

For some ontologies, I definitely want to add the SSSOM mappings, but this one here is a bit of an odd one out. I am definitely open to add them, just need to be careful about not making the OMO adoption process harder.

cthoyt commented 1 year ago

okay then I think we can close this issue. Thanks for the explanation