Adding obsoletion tag - Githubissues

monarch-initiative / mondo

Mondo Disease Ontology

http://obofoundry.org/ontology/mondo

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Adding obsoletion tag #7882

Closed sabrinatoro closed 3 months ago

sabrinatoro commented 3 months ago

The number of obsoletion candidates is more than that this time. If you look at the googlesheet:

Tab ROBOT_AddObsSubsetTag to add in release 2024-07 : 346 new obsoletion candidates
Tab ROBOT_AddObsTagForMerge to add in release 2024-07 : 5 new obsoletion candidates
Tab ROBOT_NewTermSplit-ObsTag to add in release 202407 : 1 new obsoletion candidate

sabrinatoro commented 3 months ago

WRT the sparql query: When adding a lot of obsoletion candidate tag, we run into failing on the ROBOT template merging because a comment already exist (for example). To facilitate this, I (with Nico's help) created a sparql query to identify the candidates which will make the ROBOT merging fail. I thought it would be a good tool to have in the repo for future use. I removed most of the MONDO:ID present in the original query because it doesn't make sense to keep them (the important and stable part of the query is everything else). I was in a hurry and did not explain everything related around this sparql query. Sorry. I hope it makes more sense now.

twhetzel commented 3 months ago

For "Tab ROBOT_AddObsSubsetTag to add in release 2024-07", should there be comments for all rows in the spreadsheet and therefore a comment: Reason of obsoletion... property on the Mondo class?

There are only 339 classes with comment: Reason of obsoletion..., but 352 classes with subset: obsoletion_candidate.

sabrinatoro commented 3 months ago

13 candidates already had a comment, so I had to add the obsoletion-related comment manually (otherwise the ROBOT merge would fail because terms have more than one comment). This is why you see 339 classes with comment: Reason of obsoletion..., but 352 classes with subset: obsoletion_candidate.