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oborel / obo-relations

RO is an ontology of relations for use with biological ontologies
http://oborel.github.io/
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2022-07-19 Release #617

Closed anitacaron closed 2 years ago

anitacaron commented 2 years ago

I can see the OMO term in the ro.owl. Maybe something is wrong with obo conversion?

shawntanzk commented 2 years ago

it seems specific to ro.obo cause ro-base.obo has the axioms so its the specific conversion

anitacaron commented 2 years ago

I don't see the OMO addition in ro-base.obo

shawntanzk commented 2 years ago

Base wont have any OMO stuff, but ro.obo should. weird.

ironically ro-base.owl has it, but not ro.obo >.< lol

anitacaron commented 2 years ago

The OMO is in the base because it's inside edit and not via an import, as you said here, @matentzn: https://github.com/oborel/obo-relations/pull/615#pullrequestreview-1035504762

The problem is with OBO conversion.

anitacaron commented 2 years ago

I can create the OMO import and rerun the release.

anitacaron commented 2 years ago

After meeting with @matentzn, we're aware that OBO format doesn't show the new annotation and consequently the terms that are using the annotation. Please avoid using OBO artefact.

shawntanzk commented 2 years ago

After meeting with @matentzn, we're aware that OBO format doesn't show the new annotation and consequently the terms that are using the annotation. Please avoid using OBO artefact.

Is the plan then just to add that in release notes?

shawntanzk commented 2 years ago

also little bit confused about the OMO import - is this just jim not putting the new OMO terms in OMO yet and the import is plans for when it moves over?

matentzn commented 2 years ago

I think the OBO artefact has been dropping a lot of stuff from RO anyways - it was always highly incomplete. It should just not be used at all, ideally we remove it, but I am not aware of anyone using it right now. We tried to understand why our specific expand annotation was removed (somehow a large portion of RO is in the owl-axioms header), but gave up. I don't think we need to add this to the release notes - this is not new at all, it was always like this.

OMO import is a placeholder for when we do the right thing with ODK.

cmungall commented 2 years ago

Can you make a separate issue for me to look at the obo format, and of course the obo format will not be dropped!

On Tue, Jul 19, 2022 at 3:48 AM Nico Matentzoglu @.***> wrote:

I think the OBO artefact has been dropping a lot of stuff from RO anyways

  • it was always highly incomplete. It should just not be used at all, ideally we remove it, but I am not aware of anyone using it right now. We tried to understand why our specific expand annotation was removed (somehow a large portion of RO is in the owl-axioms header), but gave up. I don't think we need to add this to the release notes - this is not new at all, it was always like this.

OMO import is a placeholder for when we do the right thing with ODK.

— Reply to this email directly, view it on GitHub https://github.com/oborel/obo-relations/pull/617#issuecomment-1188902466, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAMMOKWWFLVHD4TNM2QMYDVU2BY5ANCNFSM533RHGJQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

matentzn commented 2 years ago

I made an issue here, but the issue only scratches the surface: https://github.com/oborel/obo-relations/issues/618

There are other things that do not happen to want to be released properly. What is super odd though: that the OMO stuff does not at least appear in the owl-axiom header. That is odd.

cmungall commented 2 years ago

It looks like there is a separate issue with OMO that is totally unrelated to obo format - let's fix this first: