Closed cthoyt closed 1 year ago
@bpeters42 did you want to comment on this PR as a follow-up to discussion yesterday?
My musings were more about Chebi in general, and how we are locking us into a project that is not responsive. But on the other hand, there are plenty of worse relationships in RO, and this PR is consistent with what we are aiming to do in terms of moving relationships out of ontologies. So I approve.
Thank you for this guys 👍
Closes #697
This PR adds five new relationships corresponding to relationships in the ChEBI ontology as a follow-up to #662, where we added two relationships from ChEBI related to conjugate acids and bases.
For example, the relationship between a salt and a freebased compound is a "has functional parent" relationship.
A chemical with no chiral centers can not have an enantiomer. A chemical with multiple chiral centers can have multiple enantiomers, but its enantiomers are not themselves enantiomers (they are diastereomers).
This commonly refers to prototropy in which a hydrogen's position is changed, such as between ketones and enols. This is also often observed in heterocyclic rings, e.g., ones containing nitrogens and/or have aryl functional groups containing heteroatoms.
I found it pretty difficult to write good definitions of each of these relationships based on the ChEBI annotator guide because the sections on each of these first gave a really abstract definition (not specific enough), then an additional definition full of jargon (too specific), so I did my best to write human-usable definitions. These are assuming some chemistry knowledge, if desired, I can make them more accessible for a general audience (e.g., explaining the referenced chemistry concepts in full)
Each of the following has:
Discussion on March 28, 2023 RO Meeting