Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update "remove a term from the obsoletion list" #6563

Merged
merged 2 commits into from
Jan 31, 2024
Merged
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 11 additions & 1 deletion docs/editors-guide/curation-workflow-overview.md
Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,17 @@ If should be noted that every new term request will be represented as a GitHub i

### Request to remove a term from the obsoletion list

The community has at least two months to dispute the obsoletion of Mondo terms tagged for obsoletion, or to request a longer period of time before the term obsoletion is done (for example if one needs a longer period to review their annotations). All comment or request should be made by commenting on the GitHub ticket or contact the Mondo Curation team via email or Slack.
Once a Mondo term is tagged as “obsoletion candidate”, the community has two months to dispute, comment, or inquire about the obsoletion of this term. All discussions (disputes, comments, or inquiries) **must be reported on the GitHub issue** linked to the obsoletion (reported in the [obsoletion candidates report](https://github.com/monarch-initiative/mondo/blob/master/src/ontology/reports/mondo_obsoletioncandidates.tsv)). Disputes and requests to retain the term in Mondo must include the justifications below. There are two main reasons to retain a term in Mondo:
1. The **obsoletion candidate is an actual disease or a useful grouping class**, and therefore the concept should be retained in Mondo. In this case, justifications must include
1. Supporting evidence(s), such as PMID or DOI, that the term represents an actual disease concept or a grouping term used by the community at large
2. ORCID of the individual or link to the expert group requesting this removal from the obsoletion candidate list.
3. If obsoletion candidate is a grouping term:
1. report of other similar grouping terms (ie sibling terms). For example, if grouping by inheritance type, grouping terms by all inheritance types should exist).
2. Suggestions for maintaining the diseases grouped by this term
sabrinatoro marked this conversation as resolved.
Show resolved Hide resolved

Please note that a request to retain a term in Mondo does not imply that the term will not be an obsoletion candidate anymore: further discussion with the Mondo team and the user community will be required before the final decision.

2. The **obsoletion candidate is used in disease annotations**. Annotations using terms tagged for obsoletion should be reviewed and updated accordingly. We do understand that it might take longer than 2 months to review all annotations, and therefore we will accommodate requests for delaying term obsoletion up to one year (unless ongoing discussions indicate otherwise). Please note that unless there is strong evidence that the obsoletion candidate represents an actual disease or a useful grouping class (see above), obsoletion candidates will eventually be obsoleted from Mondo.
sabrinatoro marked this conversation as resolved.
Show resolved Hide resolved

## Mondo releases
- Mondo is released on a monthly basis around the 1st of each month.
Expand Down
Loading