obophenotype / obophenotype/uberon
Ensure ZFA is coherent when combined with Uberon
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- Dominant language
- Emacs Lisp
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- 1d 17h
- Merged PRs (30d)
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Description
This is high priority for GO, we need to incorporate ZFA into go-lego.owl - https://github.com/geneontology/go-ontology/pull/15289 - we can use @balhoff's workaround (see PR) where we use a special zfa_import but it would be good to fully align.
The goal is to get zfa into the go-lego.owl import. Currently when combined this leads to OWL unsatisfiable classes. As an example, see this discussion on combining WBbt + Uberon: #1405
One reason this is hard is because uberon includes a lot of constraints - spatial, taxonomic. These are often very useful. However, it could be argued they are too restrictive in places. Things like enforcing a distinction between spaces and material entities may seem overly philosophical. I think we can make this work. If we can't then we make remove some constraints.
I will later list some examples of incoherencies in this ticket.
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 reading the linked go-ontology PR and issue #1405, then inspect how ZFA is incorporated into go-lego.owl and how the special zfa_import workaround is used. The issue mentions OWL unsatisfiable classes but does not yet provide concrete incoherence examples; done would mean ZFA and Uberon are aligned in the import without those unsatisfiable classes.
Written by the indexing model from the issue text.
Assessment
- Domain
- data
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100