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geneontology / go-annotation

This repository hosts the tracker for issues pertaining to GO annotations.
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Review annotations to GO:0000717 nucleotide-excision repair, DNA duplex unwinding and related terms #5540

Open raymond91125 opened 6 days ago

raymond91125 commented 6 days ago

Dear all,

The proposal has been made to obsolete BP GO:0000717 nucleotide-excision repair, DNA duplex unwinding GO:0044806 G-quadruplex DNA unwinding GO:1905466 negative regulation of G-quadruplex DNA unwinding GO:1905467 positive regulation of G-quadruplex DNA unwinding GO:1905465 regulation of G-quadruplex DNA unwinding GO:0036292 DNA rewinding For they are MFs. see https://github.com/geneontology/go-ontology/issues/29153

Experimental annotations that need to be reviewed are here: https://docs.google.com/spreadsheets/d/1erB5WI0Z8FBHCTb3oCat92fDijtsb7u7O9-RV3dPHJE/edit?gid=0#gid=0

Impacted groups: ComplexPortal 3 UniProt 12 FlyBase 3 TAIR 1 BHF-UCL 8 -done PomBase 4 SGD 5

** Group contacts: https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv

Mappings that need to be reviewed: (InterPro2GO, UniProt-Keywords, UniRule) None

Thanks.

ValWood commented 4 days ago

Hi @raymond91125 it seems like we need a term for "guanine quadruplex resolver helicase" (both DNA and RNA) this particular activity seems to be a major activity of specific helicases including the ReqQ helicases (WRN,BLM ). Pif1 family, Fanconi Anemia Helicase J, DHX36 (RHAU, G4R1) A highly specialized RNA and DNA helicase with robust G4-resolving activity, Dna2, Subunits of the TFIIH transcription/repair complex, these helicases can unwind G4 structures in the context of transcription-coupled repair. and others.

This is useful functional context to retain. I can't find another specific term to replace GO:0044806 G-quadruplex DNA unwinding

RLovering commented 4 days ago

I agree with Val, I had deleted our GO:0044806 G-quadruplex DNA unwinding annotations although I had sometimes applied the parent term GO:0032392 DNA geometric change

raymond91125 commented 2 hours ago

Hi @raymond91125 it seems like we need a term for "guanine quadruplex resolver helicase" (both DNA and RNA) this particular activity seems to be a major activity of specific helicases including the ReqQ helicases (WRN,BLM ). Pif1 family, Fanconi Anemia Helicase J, DHX36 (RHAU, G4R1) A highly specialized RNA and DNA helicase with robust G4-resolving activity, Dna2, Subunits of the TFIIH transcription/repair complex, these helicases can unwind G4 structures in the context of transcription-coupled repair. and others.

This is useful functional context to retain. I can't find another specific term to replace GO:0044806 G-quadruplex DNA unwinding

@ValWood Would you make a new term request, please?