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information-artifact-ontology / ontology-metadata

OBO Metadata Ontology
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Add INN synonym type #150

Closed cthoyt closed 8 months ago

cthoyt commented 9 months ago

Closes #149

This PR adds a synonym type International Nonproprietary Name (OMO:0003010) This is mapped in the SSSOM file to the ChEBI hash URI http://purl.obolibrary.org/obo/chebi#INN

One question for @matentzn: I would like to add a synonym for this synonym type for its abbreviation (INN). Is it more work than its worth to extend the template to enable this?

cthoyt commented 9 months ago

@matentzn there are already many very specific synonyms floating around in OBO world, and they need just as much standardization love as the others.

If there's a specific issue with using a hierarchy to group synonym types, then I can remove this, but the point is that there are several other chemical synonym types that are relevant including the ones discussed in #148 and more (e.g., IUPAC)

cthoyt commented 9 months ago

@mcourtot might be able to comment in the mean time

balhoff commented 9 months ago

Have you tried nested synonym types in OBO format ontologies? I never have. @balhoff should also take a look at this,

@matentzn I'm not sure I understand the question. @cthoyt could you write out an example?

matentzn commented 9 months ago

Inn sub chemicalsyntype sub oio:synonymtype - that ok for the current obo format parser?

matentzn commented 9 months ago

If you want to move this forward you have three options:

  1. Either get an answer from Jim or Chris on whether the OBO format parser permits a nested synonym type hierarchy
  2. Write a test that proves that it is allowed
  3. remove the chemical synonym property
cthoyt commented 9 months ago

@matentzn you hashtag handled me :p. you know that I will always choose the option that gets the PR in fastest. I removed the nested hierarchy term and updated the description of the PR accordingly. We can move the discussion about adding structure within this hierarchy to a new issue.

matentzn commented 9 months ago

This PR can be merged by anyone from Wednesday 10am PT and is open for reviews until then.