Migrate repo to ODK 1.5

[matentzn]

No description provided.

[matentzn]

Changed the dc elements namespace to dc terms throughout to satisfy a new, default QC check in ODK 1.5.

[matentzn]

Updated ro import according to new spec #260

[jamesaoverton]

I think this is mostly fine but I'm worried about cob-base.owl.

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

This is what I did:

1. make a fresh clone
2. switch to this branch
3. cd src/ontology/
4. ./run.sh make all

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.

Then I look at the diffs in the generated files:

• cob.owl, cob-full.owl and cob-native.owl have minor differences that make sense -- good
• src/ontology/imports/omo_import.owl has a lot of additions, which I guess is fine
• src/ontology/imports/ro_import.owl has minor changes that I understand -- good
• 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
  • drops assertions entirely about COB, e.g. COB:0000016's inverse is COB:0000086

[matentzn]

@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]

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!

[jamesaoverton]

Is this superseded by #275, and maybe #279?

[matentzn]

Yes, I forgot this existed and scrambled to migrate your feedback over to main now, #279