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Add INN synonym type #150

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cthoyt
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@cthoyt cthoyt commented Sep 30, 2023

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?

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Have you tried nested synonym types in OBO format ontologies? I never have. @balhoff should also take a look at this, and @cmungall because this may open the flood doors to a lot of very specific synonym types, and I cant approve of this all alone..

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cthoyt commented Oct 3, 2023

@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)

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cthoyt commented Oct 4, 2023

@mcourtot might be able to comment in the mean time

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balhoff commented Oct 5, 2023

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?

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matentzn commented Oct 5, 2023

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

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matentzn commented Oct 8, 2023

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

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cthoyt commented Oct 8, 2023

@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.

@cthoyt cthoyt mentioned this pull request Oct 8, 2023
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matentzn commented Oct 9, 2023

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

@matentzn matentzn merged commit 7fa7ba2 into information-artifact-ontology:master Oct 12, 2023
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NTR: International Nonproprietary Name
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