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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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NTR: Add conjugate acid and base relations #662

Closed cthoyt closed 1 year ago

cthoyt commented 1 year ago

This PR closes #643 by adding five relationships:

CURIE Label Reason
RO:0018034 is protonated form of Transitive relationship, mirrors http://purl.obolibrary.org/obo/chebi#is_conjugate_acid_of
RO:0018033 is deprotonated form of Transitive relationship, mirrors http://purl.obolibrary.org/obo/chebi#is_conjugate_base_of
RO:0018032 is direct conjugate acid of Corresponds to a one proton change, not transitive.
RO:0018031 is direct conjugate base of Corresponds to a one proton change, not transitive.
RO:0018030 chemical relationship Groups the previous two relations, and can be used to group future relations ported out of the ChEBI handbook, similarly to how disease relationship (RO:0040035) groups various disease relationships. If this is too general, we could rename it to in protonation relationship with

This PR does not port the oboInOwl:is_cyclic and oboInOwl:is_transitive that were originally in the ChEBI RDF based on suggestions from Jim.

This PR uses the design pattern described in https://oborel.github.io/obo-relations/direct-and-indirect-relations/

cthoyt commented 1 year ago

@balhoff thanks for the feedback. I'm happy to remove these - I just wanted to bring these from the ChEBI RDF to make it maximally compatible. I'm also not aware of what is_cyclic means, so this is probably good for simplification purposes too.

Done in https://github.com/oborel/obo-relations/pull/662/commits/c8040104e2f3d78dc937e4e5751b12506ef12aab

cmungall commented 1 year ago

See my comments on transitivity on the original issue - this is nuanced, we should try and get consensus on this first

ddooley commented 1 year ago

Discussed on Jan 31 call: This pull request involves intransitive versions and so is fine to go as is, but labels then may have different semantics from CHEBI's versions. @cthoyt could you contact CHEBI about whether they can adjust/clarify transitive versions? If they are able to respond quickly then that would proactively prepare for this relationship change, and their adoption of it.

Jie suggests editor note that transitivity was removed from these relations in case others have been using CHEBI version.

Previously discussed on Jan 3 2023.

cthoyt commented 1 year ago

@ddooley will do! Sorry I couldn't attend tonight and give an update. I'll reached out to @amalik01 by email and will report back on what he says when I hear back.

cthoyt commented 1 year ago

Got generally positive feedback from Adnan Malik (ChEBI) and Andrew R Leach (Rhea) but this is not necessarily a priority for them during the ChEBI 2.0 project. We're still waiting to hear some feedback from Chris's discussion with Alan Bridge and the Rhea team, then this can probably move forwards.

cmungall commented 1 year ago

unfortunately I did not get a chance to discuss

cthoyt commented 1 year ago

Great, I was thinking we could add some sparql validations for this.

matentzn commented 1 year ago

There was no further concern (during todays RO call) with this PR, but see #691