obophenotype / obophenotype/uberon
Ensure EMAPA+Uberon combo is coherent for GOCAM pipeline
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- Emacs Lisp
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- Avg merge
- 1d 17h
- Merged PRs (30d)
- 5
Description
For Noctua GOCAMs our import chain includes both EMAPA and Uberon. Currently the combo is incoherent (OWL term for has unsatisfiable classes). If any of these are used directly or indirectly in a GOCAM, the GOCAM becomes inconsistent, and the loading of that into amigo is skipped. cc @kltm
We could just turn off uberon constraints but these are useful for error checking, so let's try resolving the issues. @ukemi will help @tfhayamizu with this.
The protocol is that if this job is red
https://build.berkeleybop.org/job/check-combined-noctua-models/
download debug.owl from
https://build.berkeleybop.org/job/check-combined-noctua-models/lastBuild/
run reasoner and get explanation for all classes under Nothing in inferred view. @ukemi is experienced with this but there are some complication here
This is an example explanation

there is no way to tell EMAPA classes from Uberon ones here. I don't have a good solution yet
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 the check-combined-noctua-models job and download debug.owl from its last build when the job is red. Run a reasoner and inspect the inferred view for all classes under Nothing, using the example explanation as a guide. Done means resolving the EMAPA/Uberon incoherence so GOCAMs load into amigo without disabling Uberon constraints.
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
- 20/100