obophenotype / obophenotype/chiro
Inhibitor hierarchy of CHEBI now mirrors EC; automate axiomatization
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Description
Some of the axioms based on previous labels may be wrong
E.g.
CHEBI:38234 used to be 'DNA polymerase inhibitor'
Now it has changed to the more specific:
CHEBI:38234 ! EC 2.7.7.7 (DNA-directed DNA polymerase) inhibitor
The reasoner is currently placing CHEBI:38234 as a superclass of CHEBI:59897 ! EC 2.7.7.49 (RNA-directed DNA polymerase) inhibitor --- which is no longer valid with the new label.
See also: https://sourceforge.net/p/chebi/curator-requests/2492/
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by comparing the current axioms for CHEBI:38234 and CHEBI:59897 with their updated labels and the linked CHEBI curator request. Determine how CHIRO currently generates or maintains the inhibitor hierarchy, then define automation that avoids the invalid superclass relation and verify the reasoner produces the corrected hierarchy.
Written by the indexing model from the issue text.
Assessment
- Domain
- data
- Issue type
- Bug
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100