INCATools / INCATools/ontology-development-kit

Add clarification re Basic modules

Open
#1,016 0 comments 0 reactions 0 assignees View on GitHub
documentation
Dominant language
Dockerfile
Stars
375
Forks
69
Avg merge
3d 5h
Merged PRs (30d)
7

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

Open the contributing 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

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.