Comments (2)
Perhaps I should try https://robot.obolibrary.org/reduce
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In our branch #81 @LilyAndres and I have found a solution that makes a reasoned product from the chemical concentration terms using nutritional_components_framework to reason it and figure out the inferred subclass relationships. This gives the reasoned end product look of a clearer hierarchy which is much easier for non-ontologists such as data curators to look at.
Unfortunately the above process removed the equivalence class expressions (the equivalence classes) and replaced them with just the inferred class relationships as asserted subclass axioms. This explains why CDNO's chemical concentration terms look the way the do in OLS after reasoning. The "duplications" show up due to having multiple parents. For example concentration of catechin in material entity
has two parents concentration of hydroxyflavan in material entity
and concentration of
the latter being inferred from the equivalence class during the release process (where we make the final cdno.owl file).
I don't' think it's possible to preserve the equivalence classes and also have the cleaner looking final hierarchy. I could be wrong but I don't think so. Assuming that's true then we have a decision to make. Do we either:
- Maintain the status quo with the equivalence classes expressions that make for a less human friendly looking hierarchy (where duplicative parents all show up)?
Or 2) Ditch the equivalence classes expressions in favor of the asserted subclasses in the final cdno-edit file which makes for a cleaner looking hierarchy for humans to search through. Note we'd still using the equivalence classes expressions in the earlier steps to figure out the hierarchy, we'd just not be showing them in the final product. The very long tail downside to this is that it wouldn't be as easily mapped to other owl ontologies that use the same design pattern for the equivalence axioms using the predicate owl:equivalence. This isn't a concern now but in the future I could see that being possible.
@Graham-J-King @maweber-bia @ddooley @ramonawalls or others please let us know what you think.
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Related Issues (20)
- Error in the design pattern during the release HOT 12
- version IRI in OLS does not resolve HOT 14
- duplicate terms under different ids now under 'concentration of' HOT 18
- xrefs are malformed - CURIEs should not have space after the colon HOT 1
- Multiple labels for ChEBI chemicals HOT 13
- Update CDNO/tooling to lastest owl API HOT 7
- Add term deprication/obsolete template HOT 2
- Create CDNO annotation documentation HOT 2
- Lignin should be a subclass of insoluble fibre? HOT 3
- Addition of dietary energy and related terms to CDNO HOT 1
- protein class suggested updates HOT 1
- floating term at top level PR_000000001 HOT 1
- Update USDA compoent prefix in mappings HOT 3
- CDNO Ontology Description missing from OLS HOT 1
- Suggestion to update template for consistency HOT 1
- Suggestion to import vitamin (role) from ChEBI
- Change parent terms for amino acid HOT 1
- Synonyms in nutritional_components_framework.csv template overriding imported synonyms HOT 1
- CDNO has some CHEBI terms with right bracket hidden in URI HOT 9
- Dietary Fiber Ontology Working Group: Fiber term updates HOT 6
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