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geneontology / go-annotation

This repository hosts the tracker for issues pertaining to GO annotations.
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IGNORE Review annotations to GO:0003964 RNA-directed DNA polymerase activity #5334

Closed pgaudet closed 1 month ago

pgaudet commented 2 months ago

Dear all,

The proposal has been made to obsolete GO:0003964 RNA-directed DNA polymerase activity & replace it by its parent

GO:0003720 telomerase activity see https://github.com/geneontology/go-ontology/issues/28394

Annotations and mappings are here: https://docs.google.com/spreadsheets/d/1gNyw7L9MoHdaNR5TrUSemkh730D9C0Ln_z-_8i1mGZg/edit?gid=0#gid=0

pgaudet commented 2 months ago

Annotations: BHF-UCL 4 CACAO 1 PomBase 1 SGD 2 UniProt 5

will be replaced automatically

Extensions: all BHF: will be replaced automatically

pgaudet commented 2 months ago

Mappings that need editing:

ValWood commented 2 months ago

What about reverse trancriptases (for example viral, or as part of transposons? ( have used for transposons)

deustp01 commented 2 months ago

What about reverse trancriptases

The difference is the source of the RNA primer - an enzyme-associated short RNA for the telomerase and a viral genomic RNA for the reverse transcriptase.

ValWood commented 2 months ago

But the term GO:0003964 RNA-directed DNA polymerase activity was agnostic for primer source?

In fact the term has 2 synonyms

RNA-directed DNA polymerase, group II intron encoded | narrow RNA-directed DNA polymerase, transposon encoded | narrow

deustp01 commented 2 months ago

Indeed. Should be GO:0003964 RNA-directed DNA polymerase activity be retired, or should terms like telomerase activity (and others that differ by the RNA template used in the activity) be made children of it? For aspects of DNA synthesis enabled by viral reverse transcriptase, I don't see how to avoid use of GO:0003964 RNA-directed DNA polymerase activity. GO:0003964 is an is_a child of GO:0034061 DNA polymerase activity - there are no terms of intermediate granularity. Do we indeed want to lump everything that uses any sort of RNA template into one term?

For example, Reactome uses this term for a step in reverse transcription of the HIV genome - R-HSA-164520 "Minus strand DNA synthesis resumes". Do we really want to assert that this is a kind of telemere elongation?

pgaudet commented 1 month ago

Apologies - this was NOT the right term. The term to be obsoleted is GO:0003721 telomerase RNA reverse transcriptase activity

I will open a new ticket.