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