obophenotype / obophenotype/uberon

Add spatial disjointness axioms between major organs

Open
#2,177 7 comments 0 reactions 2 assignees View on GitHub

@aleixpuigb is already working on this.

Since Aug 15, 2023.

Dominant language
Emacs Lisp
Stars
163
Forks
43
Avg merge
1d 17h
Merged PRs (30d)
5

Description

example problem: penicillar artery is inferred to be part of both spleen and aorta. These kinds of errors creep in due to confusion about branching-part-of vs connecting-part-of:

https://github.com/obophenotype/uberon/wiki/Branching-structures-Design-Pattern

Local decisions may look fine on the surface but global implications are clearly wrong

We could catch many of these with organ spatial/part disjointness https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern

most organ pairs should be spatially disjoint. Due to arbitrariness in what is an organ, there may be exceptions

What is the most efficient way to curate these? We could simply have a matrix of (N^2)/2 pairs and curate them (start by default assuming disjointness, and remove where we see exceptions). Similar strategy to https://pubmed.ncbi.nlm.nih.gov/32875947/

It may be better to lump into groups to hierarchically partition the space but I am not sure how best to do that. Recall most anatomical systems are not-part-disjoint as there are often interfaces

one way to partition is by vessels

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.