INCATools / INCATools/ontology-development-kit
Make subset the default method for using robot extract
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- Dominant language
- Dockerfile
- Stars
- 375
- Forks
- 69
- Avg merge
- 3d 5h
- Merged PRs (30d)
- 7
Description
Although SLME guarantees entailment preservation, paradoxically it can lead to ontologies that are *more incomplete*.
For example, currently CL and UBERON have large confusing incomplete sections in them, see:
- https://github.com/PROconsortium/PRoteinOntology/issues/307
I believe the reason GO and others don't have this is because our pipeline bypasses standard extract mechanisms and first makes a super-light version of PR
On top of this, users almost never want the additional terms from SLME. the graph method in SLME is intuitive and easy for people to understand (although of course I would love to move away from the extract-merged owl file being the default and using base modules all the way for anything user facing, but this will take longer)
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 tracing how ROBOT extract currently selects and defaults its SLME and graph methods; the issue names no files, tests, or entry points. Compare the existing subset and merged extraction behavior, then confirm that subset is the default method and that the affected extraction workflows retain their intended results.
Written by the indexing model from the issue text.
Assessment
- Domain
- tooling
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100