INCATools / INCATools/kgcl

Add a variant of the obsoletion workflow to add OBSOLETE to definition

Open
#71 0 comments 0 reactions 0 assignees View on GitHub
Dominant language
Python
Stars
23
Forks
5
PR merge metrics
No merged PRs in 30d

Description

When GO obsoletes a term the string OBSOLETE is added to the definition:

https://wiki.geneontology.org/Ontology_meeting_2024-04-08#Obsoletion

Some ontologies adopt this, others don't. Some do it half hearted. E.g. half of CL obsoletions have this and half don't. This kind of random patchwork confuses users.

In contrast OBO ontologies will always include obsolete in the label

This issue is to gather feedback from different ontologies about what their preferred policy is for this. Ideally we can achieve consensus and have a single KGCL workflow for all ontologies. I think this is best for users, as well as for maintenance. If not, then we can make this configurable.

My own preference is to keep things simple. "obsolete" in the label is sufficient. The definition is not necessarily obsolete. But the GO editors may have reasons to keep this.

Contributor guide

Open the contributing guide

Research direction

The issue does not name a file, test, or entry point. First gather feedback from the affected ontologies and resolve whether the workflow should consistently add OBSOLETE to definitions or support configuration; implementation can be scoped after that policy decision.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
20/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.