Obsolete MF-type process term involved in process

[ValWood]

Chatting with Pascale about https://github.com/geneontology/go-ontology/issues/14030 resolution

GO:0042787 protein ubiquitination involved in ubiquitin-dependent protein catabolic process which is really the same as protein ubiquitin ligase part_ of ubiquitin-dependent protein catabolic process

Might be a good time to deal with all terms of this type:

These are the "phosphorylation" ones, for example:

Especially if we do decide eventually to remove single cell process from BP https://github.com/geneontology/go-ontology/issues/12859 This could be a "fist step" in this direction. It would be a good way to focus people to see if the terms are required (and remove many of the EXP annotations, so we can see what is left)

[pgaudet]

Hi @ValWood Is there anything to do here?

[ValWood]

I thought we were going to try to get rid of "protein modification involved in blah" in favour of
MF ubiquitin ligase part_of BP ubiquitin-dependent catabolic process.

I even thought we had already don the "protein ubiquition involved in " ones but PomBase still has quite a lot....

[ValWood]

This is a baby step towards https://github.com/geneontology/go-ontology/issues/12859

can discuss next week.

[ValWood]

There is very little EXP annotation to the "protein phosphorylation involved in"

1 CDC28 involved_in GO:1990801 protein phosphorylation involved in mitotic spindle assembly could be CDC28 protein serine/threonine kinase involved_in involved in mitotic spindle assembly

GO:1902002 protein phosphorylation involved in cellular protein catabolic process 6 annotations SGD only CDC2 and MCk1

GO:1990803 protein phosphorylation involved in DNA double-strand break processing 1 annotation SGD CDC28

GO:1990802 protein phosphorylation involved in DNA double-strand break processing 1 annotation SGD CDC28

all could be protein kinase part of DNA double-strand break processing etc if SGD @srengel agree.

This would allow us to stem any proliferation of this branch.

PomBase already have lots of "protein kinase, substrate, involved in process" of this type for CDC28 ortholog Cdc2

https://www.pombase.org/gene/SPBC11B10.09

[srengel]

these suggested changes sound fine to me. i'll take a closer look, will update annotations, then will post here what i did...

[srengel]

CDC28 had 6 annotations to terms like 'protein phosphorylation involved in blah'. i changed them all to the equivalent 'blah' term:

protein phosphorylation involved in cellular protein catabolic process |   | IMP | SGD | 2015-07-14 | has direct input P34233 | Liu Q, et al. (2011)PMID:21098119 protein phosphorylation involved in cellular protein catabolic process |   | IGI with P38634 | SGD | 2015-07-14 | has direct input P38634 | Kõivomägi M, et al. (2011)PMID:21993622 protein phosphorylation involved in mitotic spindle assembly |   | IGI with P30283 | SGD | 2015-08-11 | has direct input P50275 | Juanes MA, et al. (2011)PMID:21558801 protein phosphorylation involved in DNA double-strand break processing |   | IMP | SGD | 2015-08-11 | has direct input P38859 | Chen X, et al. (2011)PMID:21841787 protein phosphorylation involved in protein localization to spindle microtubule |   | IMP | SGD | 2015-08-11 | has direct input P38991 | Zimniak T, et al. (2012)PMID:22521784 protein phosphorylation involved in double-strand break repair via nonhomologous end joining

[srengel]

updated the 4 MCK1 annotations to cellular protein catabolic process GO:0044257.

i didn't see any annotations like 'protein phosphorylation involved in blah' to budding yeast CDC2 (aka POL3). maybe that was a typo and it was only CDC28 and MCK1?

anyway, i think my action is done. if i missed something please let me know.

[ValWood]

Obsolete the following GO:1990801 protein phosphorylation involved in mitotic spindle assembly GO:1990802 protein phosphorylation involved in DNA double-strand break processing GO:1990804 protein phosphorylation involved in double-strand break repair via nonhomologous end joining GO:1990803 protein phosphorylation involved in protein localization to spindle microtubule GO:1902002 protein phosphorylation involved in cellular protein catabolic process (now have no annotations)

Good to get rid now SGD and PomBase have migrated annotations before others use....

[pgaudet]

Dear all,

The proposal has been made to obsolete the following terms: GO:1990801 protein phosphorylation involved in mitotic spindle assembly GO:1990802 protein phosphorylation involved in DNA double-strand break processing GO:1990804 protein phosphorylation involved in double-strand break repair via nonhomologous end joining GO:1990803 protein phosphorylation involved in protein localization to spindle microtubule GO:1902002 protein phosphorylation involved in cellular protein catabolic process

The reason for obsoletion is that they should be captured with a GO-CAM model. All existing manual annotations have been removed. There are no InterPro2GO mappings to this term. Any comments can be added to the issue: https://github.com/geneontology/go-ontology/issues/14137.

We are opening a comment period for this proposed obsoletion. We'd like to proceed and obsolete this term on April 11, 2018. Unless objections are received by April 11, 2018, we will assume that you agree to this change.

Thanks,

Pascale