Non-descriptive terms need "do not annotate" tag

[suzialeksander]

From the inferred annotations in the SGD load, the following terms need the DO_NOT_ANNOTATE tag same as https://github.com/geneontology/go-ontology/issues/27054#issuecomment-1964704962

• [ ] GO:0042918 alkanesulfonate transport'
• [ ] GO:0042959 alkanesulfonate transmembrane transporter activity'
• [x] GO:0061425 positive regulation of ethanol catabolic process by positive regulation of transcription from RNA polymerase II promoter
• [ ] GO:0071705 nitrogen compound transport
• [ ] GO:0072337 modified amino acid transport
• [ ] GO:1900068 negative regulation of cellular response to alkaline pH
• [ ] GO:1900070 negative regulation of cellular hyperosmotic salinity response
• [ ] GO:1900072 positive regulation of sulfite transport
• [ ] GO:1903047 mitotic cell cycle process

[pgaudet]

Obsolete GO:0061425 positive regulation of ethanol catabolic process by positive regulation of transcription from RNA polymerase II promoter as part of tx refactoring https://github.com/geneontology/go-ontology/issues/12739

[ValWood]

I'll try to do all the do_no_annotate tickets with ontobot tomorrow

[ValWood]

This didn't work? at least I don't see the do not annotate subset on GO:0042918 alkanesulfonate transport'

Also I was wondering about adding to GO:1900068 negative regulation of cellular response to alkaline pH GO:1900070 negative regulation of cellular hyperosmotic salinity response GO:1900072 positive regulation of sulfite transport

these are leaf node terms, if we don't want them to be used, presumably they should be obsoleted, not blocked?

[pgaudet]

Hi Val,

Yes leaf terms should not have 'do not annotate'. But are these terms used for annotation? ('regulation of response' is quite dubious, but we need to also focus on the open/ongoing projects, this can be done at a later point.)

Here we should try to figure out why SGD is getting inferences, it may be a weird parent ?

I noticed GO:0042918 alkanesulfonate transport' was used for annotation, did you check that the annotation could be replaced?

Thanks, Pascale

[ValWood]

I didn't see any direct annotations to GO:0042918 alkanesulfonate transport' in QuickGO, but I dodn't check thoroughly becuuse I thought you had approved, but now I see it was me doing the thumbs up!

This raises a problem though- if these were a response to incorrect inferred annotations. We can't block terms only because of an annotation transfer violation. @suzialeksander in these cases you need to report the specific violations on the curation tracker: https://github.com/geneontology/go-annotation/issues

The fix will need to be either i) inference pipeline fix ii) underlying annotation fix iii) taxon restriction or iv) obsoletion

I agree that GO:0071705 nitrogen compound transport GO:0072337 modified amino acid transport seem general enough to be blocked, so I will check how many annotations would be affected by these additions.

[pgaudet]

See https://github.com/geneontology/go-ontology/issues/27347