obophenotype / obophenotype/uberon
Xrefs without prefixes in OBO export
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- Dominant language
- Emacs Lisp
- Stars
- 163
- Forks
- 43
- Avg merge
- 1d 17h
- Merged PRs (30d)
- 5
Description
Uberon term
UBERON:0004361 (and many others)
Bug description
There is an xref appearing in OBO as xref: Stylohyoid:ligament. This doesn't have an apparent prefix, but uses the colon so Stylohyoid gets parsed as the prefix. This happens hundreds of times throughout UBERON. I think it's possible that this is the Wikipedia page, but with the underscores replaced by colons (maybe an artifact of the PURL system using underscores instead of colons, but now I'm grasping at straws)
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 with Uberon term UBERON:0004361 and compare its source xrefs with the generated OBO export, focusing on values such as Stylohyoid:ligament. Trace how these xrefs are produced and determine the intended handling of colon-containing references; the work is done when affected exports preserve valid identifiers without unintended prefix parsing.
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
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100