Obsoletion request: GO:0036261 7-methylguanosine cap hypermethylation

[ValWood]

Please provide as much information as you can:

• GO term ID and Label GO:0036261 7-methylguanosine cap hypermethylation

currently this represents a single step, the conversion of a "7-(mono)methylguanosine (m(7)G) cap" to a 2,2,7-trimethylguanosine cap structure.

The proposal is to make 2 new terms snoRNA 2,2,7-trimethylguanosine (TMG) cap formation snRNA 2,2,7-trimethylguanosine (TMG) cap formation

to replace this term.

Annotations should be made to the MF term and snoRNA 2,2,7-trimethylguanosine (TMG) cap formation

but the new terms, instead of representing only a single step in the pathway can be used to annotate all of the steps in sn/sno capping (including the 3 steps shared with mRNA capping) so that the entire pathway can be reconstituted unambiguously.

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

  • [x] The reason for obsoletion is that this represents a molecular function

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

Action https://github.com/geneontology/go-ontology/issues/26940 first

• "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 (go-friends@mailman.stanford.edu)
• [ ] paste the text in the ontology ticket

[ValWood]

I need to check where this modification occurs (I read that it occurs later in cytoplasm, so this does not seem to be part of the co-transcriptional processing pathway), it might be better to keep it separate:

if the conversion of 7-methylguanosine (m7G) cap to the 2,2,7-trimethylguanosine (TMG) cap happens in the nucleus we can stick with the original plan