Review annotations to GO:0032508 DNA duplex unwinding and related terms

[raymond91125]

Dear all,

The proposal has been made to obsolete GO:0032508 DNA duplex unwinding GO:1905462 regulation of DNA duplex unwinding GO:1905463 negative regulation of DNA duplex unwinding GO:1905464 positive regulation of DNA duplex unwinding GO:1905774 regulation of DNA helicase activity GO:1905775 negative regulation of DNA helicase activity GO:1905776 positive regulation of DNA helicase activity GO:0006268 DNA unwinding involved in DNA replication >> replace by 'DNA replication' GO:1902297 cell cycle DNA replication DNA unwinding >> replace by cell cycle DNA replication GO:1902332 bacterial-type DNA replication DNA duplex unwinding >> replace by bacterial-type DNA replication GO:1902320 nuclear DNA replication DNA duplex unwinding >> replace by GO:0033260 nuclear DNA replication GO:1902971 mitotic DNA replication DNA duplex unwinding >> replace by GO:1902969 mitotic DNA replication GO:1902970 premeiotic DNA replication DNA duplex unwinding >> replace by GO:0006279 premeiotic DNA replication see https://github.com/geneontology/go-ontology/issues/29153

Experimental annotations that need to be reviewed are here: https://docs.google.com/spreadsheets/d/1GqCxjAkMNj7zGdxZvefXCQYK0VAdix5ytp2tJl4PFI8/edit?gid=0#gid=0

Impacted groups: CACAO 3 ComplexPortal 62 EcoCyc 7 @amandamackie FlyBase 10 done MGI 12 done SGD 37 TAIR 13 UniProt 39 @Antonialock ~PomBase 13~ DONE BHF-UCL 13 -done DisProt 2 @federicaquaglia
GOC 4 GO_Central 1 GeneDB 7 @uliboehme RGD 1 DONE CGD 1 @jlewsmith

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

Mappings that need to be reviewed: (InterPro2GO, UniProt-Keywords, UniRule) @sarach06 @pedruzzi GO:0006268 interpro2go InterPro:IPR003176 Adenovirus DNA-binding, all-alpha domain > GO:DNA unwinding involved in DNA replication ; GO:0006268 GO:0006268 interpro2go InterPro:IPR005751 ATP-dependent DNA helicase PcrA > GO:DNA unwinding involved in DNA replication ; GO:0006268 GO:0006268 interpro2go InterPro:IPR005752 ATP-dependent DNA helicase Rep > GO:DNA unwinding involved in DNA replication ; GO:0006268 GO:0006268 interpro2go InterPro:IPR005753 DNA helicase, ATP-dependent, UvrD type > GO:DNA unwinding involved in DNA replication ; GO:0006268 GO:0006268 interpro2go InterPro:IPR037540 DNA-binding protein, Adenovirus > GO:DNA unwinding involved in DNA replication ; GO:0006268 GO:0006268 unirule2go UniRule:UR000036432 > GO:DNA unwinding involved in DNA replication ; GO:0006268 GO:0006268 unirule2go UniRule:UR000100683 > GO:DNA unwinding involved in DNA replication ; GO:0006268 GO:0006268 unirule2go UniRule:UR000102766 > GO:DNA unwinding involved in DNA replication ; GO:0006268 GO:0006268 unirule2go UniRule:UR000161582 > GO:DNA unwinding involved in DNA replication ; GO:0006268 GO:0006268 unirule2go UniRule:UR000165711 > GO:DNA unwinding involved in DNA replication ; GO:0006268 GO:0006268 hamap2go HAMAP:MF_00132 > GO:DNA unwinding involved in DNA replication ; GO:0006268 GO:0006268 hamap2go HAMAP:MF_00322 > GO:DNA unwinding involved in DNA replication ; GO:0006268 GO:0006268 hamap2go HAMAP:MF_00983 > GO:DNA unwinding involved in DNA replication ; GO:0006268 GO:0006268 hamap2go HAMAP:MF_01125 > GO:DNA unwinding involved in DNA replication ; GO:0006268 GO:0006268 hamap2go HAMAP:MF_01920 > GO:DNA unwinding involved in DNA replication ; GO:0006268 GO:0032508 interpro2go InterPro:IPR001208 MCM domain > GO:DNA duplex unwinding ; GO:0032508 GO:0032508 interpro2go InterPro:IPR005259 Primosomal protein N' > GO:DNA duplex unwinding ; GO:0032508 GO:0032508 interpro2go InterPro:IPR006345 ATP-dependent RecD2 DNA helicase > GO:DNA duplex unwinding ; GO:0032508 GO:0032508 interpro2go InterPro:IPR031327 Mini-chromosome maintenance protein > GO:DNA duplex unwinding ; GO:0032508 GO:0032508 interpro2go InterPro:IPR046393 Bacteriophage T4 DnaB-like replicative helicase > GO:DNA duplex unwinding ; GO:0032508 GO:0032508 unirule2go UniRule:UR000523870 > GO:DNA duplex unwinding ; GO:0032508 GO:0032508 unirule2go UniRule:UR001528770 > GO:DNA duplex unwinding ; GO:0032508 GO:0032508 unirule2go UniRule:UR001528773 > GO:DNA duplex unwinding ; GO:0032508 GO:0032508 hamap2go HAMAP:MF_04054 > GO:DNA duplex unwinding ; GO:0032508 GO:0033260 interpro2go InterPro:IPR047949 Dual specificity protein phosphatase PPS1, dual specificity phosphatase domain > GO:nuclear DNA replication ; GO:0033260 GO:1905775 interpro2go InterPro:IPR008045 DNA replication licensing factor Mcm2 > GO:negative regulation of DNA helicase activity ; GO:1905775

Thanks.

[pgaudet]

@raymond91125

The spreadsheet also contains the REPLACED BY terms - for example premeiotic DNA replication

Can you please remove the lines that dont need to be reviewed?

(Remember we cannot add the 'replaced_by' terms in the original comment) Thanks, Pascale

[hattrill]

Hi @raymond91125 GO:0033260 nuclear DNA replication is also on the review list, but this is listed as a 'replace by' term. Are we keeping "nuclear DNA replication"?

[pgaudet]

nuclear DNA replication is not being obsoleted - see my comment above

[hattrill]

FB done

[pgaudet]

UniProt done - except for 2 annotations by @Antonialock (also disputed in P2GO)

[RLovering]

Hi

on the review list are the following terms that are not listed above. Do these also need to be deleted?

GO:0000403 | Y-form DNA binding GO:0070337 | 3'-flap-structured DNA binding GO:0000405 | bubble DNA binding GO:0098530 | positive regulation of strand invasion

Thanks Ruth

[raymond91125]

Hi

on the review list are the following terms that are not listed above. Do these also need to be deleted?

GO:0000403 | Y-form DNA binding GO:0070337 | 3'-flap-structured DNA binding GO:0000405 | bubble DNA binding GO:0098530 | positive regulation of strand invasion

Thanks Ruth

@RLovering GO:0032508 is in the extensions.

[raymond91125]

@raymond91125

The spreadsheet also contains the REPLACED BY terms - for example premeiotic DNA replication

Can you please remove the lines that dont need to be reviewed?

(Remember we cannot add the 'replaced_by' terms in the original comment) Thanks, Pascale

Sorry for the mix up. The spread sheet and counts here are fixed. Thanks.

[RLovering]

Hi on the review list are the following terms that are not listed above. Do these also need to be deleted? GO:0000403 | Y-form DNA binding GO:0070337 | 3'-flap-structured DNA binding GO:0000405 | bubble DNA binding GO:0098530 | positive regulation of strand invasion Thanks Ruth

@RLovering GO:0032508 is in the extensions.

Oops sorry about that, all done - Ruth

[slaulederkind]

RGD finished.

[LiNiMGI]

MGI done.

[victorianugnes]

DisProt done.