Obsoletion request: GO:0006268 DNA unwinding involved in DNA replication

[ValWood]

Please provide as much information as you can:

• GO term ID and Label

GO:0006268 DNA unwinding involved in DNA replication

• Reason for deprecation Put an x in the appropriate box:

• The reason for obsoletion is that this term represents a molecular function.

• "Replace by" term (ID and label)
  If all annotations can safely be moved to that term

• "Consider" term(s) (ID and label)
  Suggestions for reannotation

• Are there annotations to this term?

• How many EXP:

• Are there mappings and cross references to this term? (InterPro, Keywords; check QuickGO cross-references section)

• Is this term in a subset? (check the AmiGO page for that term)

• Any other information

---

Checklist for ontology editor

Check term usage and metadata in Protégé

• check term usage in the ontology
• check internal mappings: RHEA, EC, MetaCyc
• check subset usage
• check taxon constraints

Check annotations

• create Annotation Review spreadsheet
• • Annotation Review template: https://docs.google.com/spreadsheets/d/1izV3q1jnq_Ybg5MJ53O_b5BCTkGtjl_Fi-cOg3-7eBE/edit#gid=0
• • Instructions: https://wiki.geneontology.org/Annotation_Review_Request
• create annotation review ticket: https://github.com/geneontology/go-annotation/issues/new?assignees=&labels=annotation+review&template=annotation-review-for-obsoletion.md&title=Review+annotations+to+%5BINSERT+GO+TERM%5D
• find external mappings (via IEAS), include in obsoletion notice
• tag curators in Annotation Review ticket. Responsible annotator for each group: https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv

Notification

• create obsoletion announcement
• announce to GO friends ([email protected])
• paste the text in the ontology ticket

[raymond91125]

To be sure. We want to obsolete all child terms as well.

• 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

[pgaudet]

Hi @raymond91125

This is right. We should also obsolete the parent GO:0032508 DNA duplex unwinding, since this is a single-step process (= DNA helicase activity), and the regulation terms:

• GO:1905462 regulation of DNA duplex unwinding
• GO:1905463 negative regulation of DNA duplex unwinding
• GO:1905464 positive regulation of DNA duplex unwinding

and regulation of DNA helicase activity: (this is covered by another ticket #22455 but since there are few annotations (3 EXP), we can deal with these now):

• GO:1905774 regulation of DNA helicase activity
• GO:1905775 negative regulation of DNA helicase activity
• [GO:1905776 positive regulation of DNA helicase activity

[raymond91125]

• GO:0032508 DNA duplex unwinding

[pgaudet]

Hi @raymond91125

We should also obsolete

• GO:0010501 RNA secondary structure unwinding

[raymond91125]

@pgaudet Should these also be obsoleted?

• 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

[pgaudet]

Yes ! I'm not sure what the G duplex is though. Should there be a process to capture that? Le ven. 15 nov. 2024, 19:13, Raymond Lee ***@***.***> a écrit :

…

@pgaudet <https://github.com/pgaudet> Should these also be obsoleted? - 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 — Reply to this email directly, view it on GitHub <#29153 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABEPWUERQIGY2UVFSQCELET2AY2V5AVCNFSM6AAAAABREKK24KVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINZXG4YDONRWGE> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[raymond91125]

PMID:25653156 via the action of a DEAH-box ATP-dependent helicase.