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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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methylation branch #27423

Open ValWood opened 3 months ago

ValWood commented 3 months ago

mRNA methylation is now gone, but it seems odd that we have the other methylation terms. @pgaudet Should this branch have "do not annotate" added, pending obsoletion?

ValWood commented 3 months ago

GO:0032259 methylation GO:0043414 macromolecule methylation

I will add to GO:0110004 biological_process positive regulation of tRNA methylation GO:0110005 biological_process positive regulation of tRNA C5-cytosine methylation GO:0110002 biological_process regulation of tRNA methylation GO:0110003 biological_process regulation of tRNA C5-cytosine methylation GO:0002131 biological_process wobble position cytosine ribose methylation GO:0002132 biological_process wobble position uridine ribose methylation GO:0002127 biological_process tRNA wobble base cytosine methylation GO:0002128 biological_process tRNA nucleoside ribose methylation GO:0002129 biological_process wobble position guanine ribose methylation GO:0106005 biological_process RNA 5'-cap (guanine-N7)-methylation GO:0106004 biological_process tRNA (guanine-N7)-methylation GO:0070475 biological_process rRNA base methylation GO:0070476 biological_process rRNA (guanine-N7)-methylation GO:0080178 biological_process 5-carbamoylmethyl uridine residue modification GO:0106349 biological_process snRNA methylation GO:0001510 biological_process RNA methylation GO:0106217 biological_process tRNA C3-cytosine methylation GO:0031167 biological_process rRNA methylation GO:0070901 biological_process mitochondrial tRNA methylation GO:0030488 biological_process tRNA methylation GO:1990437 biological_process snRNA 2'-O-methylation GO:1990438 biological_process U6 2'-O-snRNA methylation GO:0002939 biological_process tRNA N1-guanine methylation GO:0002940 biological_process tRNA N2-guanine methylation GO:0002942 biological_process tRNA m2,2-guanine biosynthesis GO:0002946 biological_process tRNA C5-cytosine methylation GO:0036265 biological_process RNA (guanine-N7)-methylation GO:0000452 biological_process snoRNA guided rRNA 2'-O-methylation GO:0000451 biological_process rRNA 2'-O-methylation

GO:0036261 7-methylguanosine cap hypermethylation 2,2,7-trimethylguanosine cap formation current exact synonym and "methylation" parent removed pending changes in https://github.com/geneontology/go-ontology/issues/26976

ValWood commented 3 months ago

@pgaudet I could do this with ontobot, but I think we should also add a comment "this term is pending obsoletion"

Ideally we would have different types of "do not annotate", I think this would be better because pending obsoletion os a very different subset.

First off, I will check how much these are used. It might be less pain to process to obsoletion.

ValWood commented 3 months ago

There are 336 EXP annotations..... block or obsolete?

ValWood commented 3 months ago

I think I will block for now, it's quite a lot but it will prevent new...

pgaudet commented 3 months ago

Will we be using the same ticket for obsoletion? Or is the current ticket only for the do_not_annotate?

ValWood commented 3 months ago

I think a new obsoletion ticket when the time comes. These would be a bit unwieldy in one ticket.