Obsoletion request: redundant descendants of [GO ID:GO:0032187 actomyosin contractile ring localization]

[ValWood]

Please provide as much information as you can: Follow on from https://github.com/geneontology/go-ontology/issues/21834

• [x] GO:0032188  establishment of actomyosin contractile ring localization Replace by -> GO:0007105 cytokinesis, division site positioning

• [x] GO:1903486 establishment of mitotic actomyosin contractile ring localization Replace by -> GO:1902408 mitotic cytokinesis, division site positioning

• [x] GO:1901648 regulation of actomyosin contractile ring localization Replace by -> GO:2000073 regulation of cytokinesis, site selection

• [x] GO:1903505 regulation of establishment of actomyosin contractile ring localization involved in mitotic cell cycle Replace by -> GO:1902472 regulation of mitotic cytokinesis, division site positioning

• [x] GO:1902471 regulation of mitotic actomyosin contractile ring localization Replace by -> GO:1902472 regulation of mitotic cytokinesis, division site positioning

• [x] GO:1901649 negative regulation of actomyosin contractile ring localization Replace by -> GO:2000075 negative regulation of cytokinesis, site selection

• [x] GO:1901650 positive regulation of actomyosin contractile ring localization Replace by -> GO:2000076 positive regulation of cytokinesis, site selection

• [x] GO:0071342 regulation of establishment of actomyosin contractile ring localization Replace by -> GO:2000073 regulation of cytokinesis, site selection

• [x] GO:1902405 mitotic actomyosin contractile ring localization Replace by -> GO:1902408 mitotic cytokinesis, division site positioning

Branch has only 10 EXP annotations 6 PomBase 1 CGD 3 FlyBase

• GO term ID and Label

• Reason for deprecation Put an x in the appropriate box:

  • [ ] The reason for obsoletion is that the term is not clearly defined and usage has been inconsistent. Also there is an additional branch with terms with he same meaning

• "Replace by" term (ID and label)

See above for replaced by

• Are there annotations to this term?
• How many EXP: 10

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Checklist for ontology editor

Check term usage and metadata in Protégé

• [x] check term usage in the ontology
• [ ] check internal mappings: RHEA, EC, MetaCyc
• [x] check subset usage
• [ ] check taxon constraints

Check annotations

• [x] create Annotation Review spreadsheet Direct replacement, no annotation review required

• [x] find external mappings (via IEAS), include in obsoletion notice

Notification

• [x] create obsoletion announcement
• [x] announce to GO friends (go-friends@mailman.stanford.edu)
• [ ] paste the text in the ontology ticket

[ValWood]

@pgaudet since this is a merge do I don't need an annotation tracker ticket, correct? Just an obsoletion notice?

[ValWood]

I will go ahead with this today since there will be automatic replacement.

[ValWood]

Check graph still need to deal with GO:0032187 | actomyosin contractile ring localization (this one has a taxon restriction)

and consider maintenance (is this a phenotype only, does the ring move unless a mutant?)

[pgaudet]

Sorry I had missed that

since this is a merge do I don't need an annotation tracker ticket, correct? Just an obsoletion notice?

You need to send a review ticket, not all groups have procedures for automated replacements. Everyone editing in Noctua and P2GO is OK; other groups need to be notified.

Thanks, Pascale

[ValWood]

So, this list will be OK? 6 PomBase 1 CGD 3 FlyBase

Which groups don't use Noctua or P2GO apart from PomBase and PHI-base, Eco-Cyc?

[pgaudet]

EcoCyc EcoWiki TAIR CGD ComplexPortal/IntAct InterPro Reactome SP keywords RNA central SynGO GeneDB HPA PseudoCAP DisProt SGN

I think that's about it

[ValWood]

Dear @marekskrzypek @jlewsmith

There is a single CGD annotation to IQG1 |   |   | actomyosin contractile ring localization |   | CGD | Candida albicans SC5314 | IMP

The branch GO:0007105 cytokinesis, division site positioning was duplicated with equivalent terms.

This term will be obsoleted with the replacement term: GO:0007105 cytokinesis, division site positioning

We can no longer merge terms which are equivalent, they need to be obsoleted.

If the term was used to describe an evolved process you can just migrate the annotation to the remaining term. Or, if the paper is describing detachment and migration of the ring after it is formed at a particular localization, this represents an aberrant mutant phenotype and not an evolved process.

[ValWood]

@hattrill just to check that you already updated your annotations as per https://github.com/geneontology/go-ontology/issues/21834 I still see them. v

[hattrill]

Hi @ValWood , Sorry, thought there was going to be a merge. Will review them now.

[ValWood]

Oh actually, it's OK, if. you use protein2GO they will be migrated to the new term. It isn't a merge but it's equivalent to a merge.

[hattrill]

Cool. Actually, good for me to look at them as one needed to be removed. All done now.

One thing I noticed was that we have a term for mitosis: mitotic cytokinesis, division site positioning but not the equivalent for the meiotic branch

might be a deliberate ommission or something that isn't needed cos of GO-CAMs...but thought that I'd mention it.

[jlewsmith]

Hi Val,

I'll take a look at the paper and make the appropriate change.

Thanks, Jodi

[ValWood]

One thing I noticed was that we have a term for mitosis: mitotic cytokinesis, division site positioning but not the equivalent for the meiotic branch

The reason for this is that most of the work on cytokinesis has been done in yeast. In yeast the process of "cytokinesis" is very different, (because basically the cell forms spores around the segregated DNA, rather than an actomyosin contractile ring and a septum). All of the yeast annotations are for mitotic cytokinesis. There are only 160 EXP annotations to meiotic cytokinesis, so I suspect it's just that the terms have not been required yet due to depth of study.

[ValWood]

Will open another ticket for the remaining 3 terms that appear to be redundant.

[ValWood]

Follow up is in https://github.com/geneontology/go-ontology/issues/25606