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
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