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_of UBERON: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

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. 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

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