obophenotype / obophenotype/uberon

Ensure EMAPA+Uberon combo is coherent for GOCAM pipeline

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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

image

there is no way to tell EMAPA classes from Uberon ones here. I don't have a good solution yet

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First steps

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  3. Fork the repository and make your change on a branch.
  4. 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

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