obophenotype / obophenotype/uberon
incorrect taxon constraints
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Description
Uberon term
cuticle development
regulation of epidermal cell differentiation
stem cell differentiation
and others....
Bug description
this is prompted by a (now very old) ticket in the GO where many plant annotations are being flagged as taxon constraint violations because of associations to UBERON terms. Pascale Guadet requested we open a ticket her in Uberon.
https://github.com/geneontology/go-ontology/issues/30555
Reviewing our latest snapshot for GO rule violations, we noticed a bunch of new taxon violations for old Arabidopsis annotations to these terms. (sample only, there are more)
cuticle development
regulation of epidermal cell differentiation
stem cell differentiation
Was there a mass mapping of some older GO terms to UBERON terms for logical defs and the GO terms then acquired their taxon constraints? Can we revisit some of these and address the taxon constraint issues?
Contributor guide
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 reviewing the listed Uberon terms and the related GO issue 30555, then inspect the taxon constraints affecting the cited Arabidopsis annotations. Compare the term mappings and logical definitions against the reported violations. Done means the affected constraints are identified and the issue records the agreed corrections or rationale for leaving them unchanged.
Written by the indexing model from the issue text.
Assessment
- Domain
- data
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 42/100