obophenotype / obophenotype/uberon
[Fix] UBERON:0003351 'pharyngeal epithelium' is chordate-restricted but generically labelled
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Description
Uberon term
UBERON:0003351
Bug description
UBERON:0003351 has the equivalence axiom epithelium and part_of some UBERON:0001042 (chordate
pharynx), but its label, its definition ("An epithelium that is part of a pharynx") and its
exact synonyms "epithelium of pharynx" and "pharynx epithelium" all read as generic. A curator
matching tissue names against labels will annotate non-chordate pharyngeal epithelium with a
class that asserts the tissue is part of a chordate pharynx. I nearly did that for a sea
cucumber sample and caught it only by reading the axioms.
- Either rename to "chordate pharyngeal epithelium" and demote the generic strings to narrow or related synonyms, or add a taxon-neutral class (epithelium
part_ofUBERON:0006562 pharynx) with UBERON:0003351 as its child. - Related: UBERON:0006562 pharynx carries
scheduled_for_obsoletion_on_or_after "2023-04-20". Is that still planned, what should curators use for a non-chordate pharynx, and is UBERON:0006562 safe to annotate with meanwhile?
ORCID: https://orcid.org/0000-0001-5025-5886. Filing on behalf of Lattice, Klein Lab, Department of Biomedical Data Science, Stanford School of Medicine.
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 equivalence axiom, label, definition, synonyms, and the status of UBERON:0006562 described in the issue. Done means the taxonomic scope is made explicit or a taxon-neutral class is established, and the issue's question about obsoletion and safe curator use has a documented decision.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Active
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100