INCATools / INCATools/ontology-development-kit
Add clarification re Basic modules
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Description
https://oboacademy.github.io/obook/reference/release-artefacts/
> The default -basic version corresponds to the -simple artefact with only 'part of' relationships (BFO:0000050)
This is potentially confusing. Most users think of "relationship" as being an edge in a graph, not as an existential restriction, so this makes it sound like we filter is-as.
Note also that releases such as uberon-basic includes quite non-basic relationships like `mutually_spatially_disjoint_with`. Yes, those of us who are OWL gurus know that this is an annotation assertion that is a shortcut for a complex OWL axiom. But for many users, this is just an edge that will confuse them.
The original basic profile was defined here:
https://owlcollab.github.io/oboformat/doc/obo-syntax.html#6
This is poorly written as it conflicts obo syntax relationships (non-is-a graph edges) with existential restrictions (these coincide 99% of the time). With the former interpretation the Uberon basic graph is not a DAG, violating basic. With the latter it is.
Contributor guide
Research direction
Start with the release-artefacts reference page linked in the issue, then compare its Basic modules wording with the original OBO syntax profile. Clarify how relationship edges, existential restrictions, and non-basic relationships such as mutually_spatial_disjoint_with are treated, while preserving the documented distinction between the interpretations.
Written by the indexing model from the issue text.
Assessment
- Domain
- documentation
- Issue type
- Documentation
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 42/100