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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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3' end processing summary and next steps.... #27055

Open ValWood opened 8 months ago

ValWood commented 8 months ago

After many single-step process obsoletions this branch is more organized:

Screenshot 2024-02-14 at 15 18 51

mRNA polyadenylation children have now all been rehoused or obsoleted (this will go in the next week or so)

Next tasks:

obsolete RNA 3' uridylation (MF)

Questions:

Do we need tRNA 3'-terminal CCA addition https://www.pombase.org/term_genes/GO:0001680 are there other parts of 3' end processing? if so what are they? At present ,we end up with mitochondrial and cytosolic tRNA processing annotated differently, even though it is the same enzymes (it seems) see e.g. https://www.pombase.org/gene/SPCC645.10

snoRNA 3' end processing- do we need separate terms for CD/Box and H/ACA box? This brings another axis of classification and so to justify, they probably need to be distinct end processing pathways? Earlier I renamed " GO:0071051 | polyadenylation-dependent snoRNA 3'-end processing

GO:0071051
polyadenylation-dependent snoRNA 3'-end processing" to co-transcriptional snoRNA 3'-end processing, cleavage and polyadenylation pathway but the annotations are to exosome subunits. The exosome isn't involved in the polyadenylation pathway AFAIK (it operates downstream if the surveillance pathway kicks in), so I need to look at the papers and see if this is actually a different pathway.

snRNA 3'-end processing Do we need the "gene product specific" children here if it is the same pathway?

I will leave "alternative polyadenylation" until later. It isn't in itself a process, it occurs in different contexts , i) as part of the regulatory switch for lncRNA-mediated gene repression, ii) but also presumably to create alternative mRNAs and likely others. We can decide later which pathways this is part of.

Finally we can decide which high-level grouping terms are unnecessary. Probably leave this until I know what edge cases we have, and that everything works for bacteria and plants before we remove anything.

Add "do not annotate" labels where appropriate.

ValWood commented 8 months ago

see https://github.com/geneontology/go-ontology/issues/27068 for sno processing