search

OBOFoundry / COB

An experimental ontology containing key terms from Open Biological and Biomedical Ontologies (OBO)
https://obofoundry.github.io/COB
Creative Commons Zero v1.0 Universal
35 stars 8 forks source link

Migrate repo to ODK 1.5 #259

Open matentzn opened 3 months ago

matentzn commented 3 months ago

@jamesaoverton for the review.

(I'm not sure how valuable my review is. I don't use ODK much, and there's just a ton of changes here.)

Very valuable. Thanks for taking the time!

That mostly works, but I get an error at https://github.com/OBOFoundry/COB/blob/odk1.5/src/ontology/cob.Makefile#L26 because products/* does not match any files. If I mkdir products && touch products/foo.bar then make all completes successfully.

I added a README.md now in there as a fixture so this should not happen again.

cob-base.owl I'm worried about drops a lot of assertions about external terms, which is good also drops important equivalence axioms and annotations on them, which I don't think is good but I'm not sure; e.g. COB:0000107 equivalent to OBI:0000070

That should not be the case.. See below, I have reverted the process for now!

drops assertions entirely about COB, e.g. COB:0000016's inverse is COB:0000086

Good spot! This is because of some missing conditionals, which we will have in the next ROBOT release: https://github.com/ontodev/robot/pull/1187/files#diff-dc25d0b1a6794b1ac6ad2d5dfa891e182bc17f72541e3ca467cb3fd7a62a1e3eR1543

I have decided to revert the COB base process to what it was before. The accompanying issue is #261. Thanks for spotting that. COB base is not that straight forward to define I guess.

matentzn commented 3 months ago

I also made sure that you and your team can run the releases again properly, by upgrading sssom py during the relevant pipeline step. I think this is ready to go now!