oborel / obo-relations

RO is an ontology of relations for use with biological ontologies
http://oborel.github.io/
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Add remaining 5 ChEBI relations #698

Closed cthoyt closed 1 year ago

cthoyt commented 1 year ago

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.

Identifier Label Description ChEBI
RO:0018038 has functional parent Chemical A has functional parent Chemical B if there is chemical transformation through which chemical B can be produced from chemical A.

For example, the relationship between a salt and a freebased compound is a "has functional parent" relationship.
http://purl.obolibrary.org/obo/chebi#has_functional_parent
RO:0018040 has parent hydride Chemical A has parent hydride Chemical B if there exists a molecular graphical transformation where functional groups on A are replaced with hydrogens in order to yield B. http://purl.obolibrary.org/obo/chebi#has_parent_hydride
RO:0018039 is enantiomer of Chemicals A and B are enantiomers if they share the same molecular graph except the change of the configuration of substituents around exactly one chiral center.

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).
http://purl.obolibrary.org/obo/chebi#is_enantiomer_of
RO:0018037 is substitutent group from Group A is a substituent group from Chemical B if A represents the functional part of A and includes information about where it is connected. A is not itself a chemical with a fully formed chemical graph, but is rather a partial graph with one or more connection points that can be used to attach to another chemical graph, typically as a functionalization. http://purl.obolibrary.org/obo/chebi#is_substituent_group_from
RO:0018036 is tautomer of Two chemicals are tautomers if they can be readily interconverted.

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.
http://purl.obolibrary.org/obo/chebi#is_tautomer_of

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:

  1. A parent relationship to "chemical relationship"
  2. Reference to original issue
  3. Example from ChEBI
  4. Attribution / date of creation
  5. Xref to equivalent ChEBI relationship

Discussion on March 28, 2023 RO Meeting

cthoyt commented 1 year ago

@bpeters42 did you want to comment on this PR as a follow-up to discussion yesterday?

bpeters42 commented 1 year ago

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.

CarMoreno commented 1 year ago

Thank you for this guys 👍