polyadenylation and cleavage

[ValWood]

It is impossible to annotate sensibly. There are has 39 process terms to choose from! I don't even know where to begin... Should be 3 or 4 processes:

1. cotranscriptional 3’ processing of RNA polymerase II transcripts (i.e nuclear polyadenylation, I think this is always coupled to termination- will check)

2. cytoplasmic polyadenylation

3. mitochondrial/bacterial

This is the left-hand frame

This is the right-hand frame

[ValWood]

There are at least 2 independent branches, there is no relationship at all between these 2 terms. The split does not seem to follow the biology in any way.

(Note, This split is actually OK. It describes the downstream pathways. polyadenylation dependent blah...."

[ValWood]

Also polyadenylation is a type of 3' end processing. But this is connection is not recognized in the BP ontology.

Suggestions

1. terms should represent the processes and not the activities. For example "nuclear cleavage and polyadenylation" is also referred to as:

"cotranscriptional 3’ processing of RNA polymerase II (Pol2) transcripts" ( the cleavage, and the polyadenylation are single steps in this process).

We need to obsolete all of the single steps and do a lot of consolidation.

[ValWood]

https://github.com/geneontology/go-ontology/issues/22708 https://github.com/geneontology/go-ontology/issues/22718 https://github.com/geneontology/go-ontology/issues/22229

[ValWood]

we also have other requests for terms which refer to the same process but described in a different way https://github.com/geneontology/go-ontology/issues/22339

We need to make it clear which terms refer to:

1. the nuclear process (cotranscriptional 3’ processing of RNA polymerase II transcript )
2. the cytoplasmic pathways because they have different purposes and outcomes.

[ValWood]

review again after the 3 tickets above are closed

[ValWood]

I don't need this ticket.