obophenotype / obophenotype/chiro
Roles doing stuff where entities should be?
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Description
It seems odd to have roles rather than entities inhibiting, activating etc.
e.g. '4-aminobutyrate transaminase inhibitor' (a CHEBI ROLE) EquivalentTO 'biological role'
and (inhibitor_of some '4-aminobutyrate transaminase activity')
This could work:
'chemical entity' that has_role some 4-aminobutyrate transaminase inhibitor' EquivalentTo inhibitor_of some '4-aminobutyrate transaminase activity'
But perhaps harder to maintain, in which case GO(CHE) style bridging classes might be a good idea.
Alternatively, in the spirit of the BFO conception of this, we might say
4-aminobutyrate transaminase inhibitor (role) EquivalentTo: realised_by some* (inhibition_of some 4-aminobutyrate transaminase activity')
(*only ??? - I don't think this is necessary if roles can be bourne without being realised)
Or combining with a typical GO way of doing things:
4-aminobutyrate transaminase inhibitor (role) EquivalentTo: realised_by some 'negative regulation of 4-aminobutyrate transaminase activity')
Perhaps some use case queries would help clarify the preferred approach.
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Research direction
No files, tests, or entry points are identified in the issue. First resolve the preferred modeling approach using the proposed CHEBI, GO, and BFO alternatives and use-case queries; the work is complete only when that approach is agreed and implemented consistently.
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Assessment
- Domain
- data
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100