Add pre obsoletion "do not annotate" flag to "regulation of modification" terms

[ValWood]

Add the pre-obsoletion do not annotate flag

GO:1904285    regulation of protein-pyridoxal-5-phosphate linkage GO:1904286 negative regulation of protein-pyridoxal-5-phosphate linkage
GO:0010799 regulation of peptidyl-threonine phosphorylation GO:0010800 positive regulation of peptidyl-threonine phosphorylation GO:0010801 negative regulation of peptidyl-threonine phosphorylation GO:1903719 regulation of I-kappaB phosphorylation GO:1903721 positive regulation of I-kappaB phosphorylation GO:1903720 negative regulation of I-kappaB phosphorylation GO:0033135 regulation of peptidyl-serine phosphorylation GO:0033137 negative regulation of peptidyl-serine phosphorylation
GO:0033138 positive regulation of peptidyl-serine phosphorylation GO:0033139 regulation of peptidyl-serine phosphorylation of STAT protein GO:0033140 negative regulation of peptidyl-serine phosphorylation of STAT protein GO:0033141 positive regulation of peptidyl-serine phosphorylation of STAT protein GO:0001934 positive regulation of protein phosphorylation GO:0001933 negative regulation of protein phosphorylation GO:0001932 regulation of protein phosphorylation GO:0043538 regulation of actin phosphorylation GO:0060734 regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation GO:0060735 regulation of eIF2 alpha phosphorylation by dsRNA GO:1904323 regulation of inhibitory G protein-coupled receptor phosphorylation GO:1904325 positive regulation of inhibitory G protein-coupled receptor phosphorylation GO:1904324 negative regulation of inhibitory G protein-coupled receptor phosphorylation GO:0010999 regulation of eIF2 alpha phosphorylation by heme GO:0031952 regulation of protein autophosphorylation GO:0050730 regulation of peptidyl-tyrosine phosphorylation GO:0031953 negative regulation of protein autophosphorylation GO:0031954 positive regulation of protein autophosphorylation GO:1900084 regulation of peptidyl-tyrosine autophosphorylation GO:1900085 negative regulation of peptidyl-tyrosine autophosphorylation GO:0061097 regulation of protein tyrosine kinase activity GO:0050732 negative regulation of peptidyl-tyrosine phosphorylation GO:0050731 positive regulation of peptidyl-tyrosine phosphorylation GO:0010533 regulation of activation of Janus kinase activity GO:0042509 regulation of tyrosine phosphorylation of STAT protein GO:1904806    regulation of protein oxidation GO:1904808 positive regulation of protein oxidation GO:1904807 negative regulation of protein oxidation GO:2000539    regulation of protein geranylgeranylation GO:2000540 negative regulation of protein geranylgeranylation GO:2000541 positive regulation of protein geranylgeranylation GO:1901983    regulation of protein acetylation GO:2000758 positive regulation of peptidyl-lysine acetylation GO:2000761 positive regulation of N-terminal peptidyl-lysine acetylation GO:2000759 regulation of N-terminal peptidyl-lysine acetylation GO:2000760 negative regulation of N-terminal peptidyl-lysine acetylation GO:2000757 negative regulation of peptidyl-lysine acetylation GO:1902390 regulation of N-terminal peptidyl-serine acetylation GO:1902391 positive regulation of N-terminal peptidyl-serine acetylation GO:1901985 positive regulation of protein acetylation GO:1901984 negative regulation of protein acetylation GO:1904663 regulation of N-terminal peptidyl-methionine acetylation GO:2000756 regulation of peptidyl-lysine acetylation GO:1904665 positive regulation of N-terminal peptidyl-methionine acetylation GO:1904664 negative regulation of N-terminal peptidyl-methionine acetylation GO:2000170 positive regulation of peptidyl-cysteine S-nitrosylation GO:1902083 negative regulation of peptidyl-cysteine S-nitrosylation GO:1904286 negative regulation of protein-pyridoxal-5-phosphate linkage GO:1904287 positive regulation of protein-pyridoxal-5-phosphate linkage GO:1904285 regulation of protein-pyridoxal-5-phosphate linkage GO:2000169 regulation of peptidyl-cysteine S-nitrosylation GO:1901873 regulation of post-translational protein modification GO:1901874 negative regulation of post-translational protein modification GO:1901875 positive regulation of post-translational protein modification GO:0060051 negative regulation of protein glycosylation GO:1904098 regulation of protein O-linked glycosylation GO:0060050 positive regulation of protein glycosylation GO:1904099 negative regulation of protein O-linked glycosylation GO:1904100 positive regulation of protein O-linked glycosylation GO:2000169    regulation of peptidyl-cysteine S-nitrosylation GO:1901873    regulation of post-translational protein modification GO:0060049    regulation of protein glycosylation GO:0031401    positive regulation of protein modification process GO:0031400    negative regulation of protein modification process GO:0035304    regulation of protein dephosphorylation GO:1903059    regulation of protein lipidation GO:1903059 regulation of protein lipidation GO:1902662 regulation of peptidyl-L-cysteine S-palmitoylatin GO:0060254 regulation of N-terminal protein palmitoylation GO:1903061 positive regulation of protein lipidation GO:1903060 negative regulation of protein lipidation GO:1902664 positive regulation of peptidyl-L-cysteine S-palmitoylation GO:1902663 negative regulation of peptidyl-L-cysteine S-palmitoylation GO:0060262 negative regulation of N-terminal protein palmitoylation GO:0120093    regulation of peptidyl-lysine crotonylation GO:0120094 negative regulation of peptidyl-lysine crotonylation GO:1903344    regulation of protein polyglycylation GO:1903346 positive regulation of protein polyglycylation GO:1903345 negative regulation of protein polyglycylation GO:0010734 negative regulation of protein glutathionylation
GO:0010733 positive regulation of protein glutathionylation GO:0010732    regulation of protein glutathionylation GO:0090311    regulation of protein deacetylation GO:0090043 regulation of tubulin deacetylation
GO:0090312 positive regulation of protein deacetylation GO:0090044 positive regulation of tubulin deacetylation GO:1900722    regulation of protein adenylylation GO:1900723 negative regulation of protein adenylylation GO:1900724 positive regulation of protein adenylylation

[deustp01]

Is there some discussion someplace of the rationale for these pre-obsoletions? Is this part of a broader clean-up? What is it aimed at? I.e., it would be really helpful to know, not just for legacy maintenance but for planning future curation, to understand what makes a process in or out of scope for GO.

[ValWood]

The "modification" branch in process has been slated for obsoletion for a long time, (was originally proposed by Suzi Lewis probably almost a decade ago and ratified in Montreal IIRC (note that the histone modifications/regulation of histone modifications are already removed). So for this particular branch I was assuming that has been fairly widely communicated for a long time.

Instead of annotating to "phosphorylation/regulation of phosphorylation", which isn't biologically informative, you would annotate to the specific process that is being regulated by the phosphorylation event (for example ", signalling pathway x and/or regulation of chromosome segregation", etc). This helps to prevent multiple different types of process annotations to describe the identical process and make annotation more consistent, and improves the biological representation.

The pre-obsoletion is just a clearer version of "do not annotate" which is applied largely to high-level grouping terms. This is effectively a heads up (soft check) to help curators make a decision when annotating and prevent new annotations accumulating until the obsoletion is eventually actioned. We have to do the obsoletions in a step-wide manner because if the entire branch was obsoleted now it would be too much work for curators to review all in one go.

Note that most of the branch already has "do not annotate" flag pending obsoletion, here I am filling in the missing 'regulation' ones (and using the more specific pre-obsoletion flag). One reason I am eager to flag these terms is to prevent function prediction annotations because it is difficult to communicate why we haven't made annotations to these terms if they are not flagged in some way.

Does that make sense? Probably this is something that should be highlighted on and annotation call @vanaukenk

[ValWood]

@pgaudet is there a quick way to add the pre-obsoletion flag to these terms?