Obsoletion request: GO:0140655 mitochondrial proliferation

[hattrill]

Obsoletion request: GO:0140655 mitochondrial proliferation

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

  • [x] The reason for obsoletion is that the term is not clearly defined and usage has been inconsistent.
  • [ ] The reason for obsoletion is that this term is pre-composed and should be represented as a GO-CAM model.
  • [ ] The reason for obsoletion is that this term represent an assay and not a GO process.
  • [ ] The reason for obsoletion is that this represents a phenotype.
  • [ ] The reason for obsoletion is that the data from the paper for which the term was requested can be accurately described using [appropriate GO term].
  • [ ] The reason for obsoletion is that this term represents a molecular function.
  • [ ] The reason for obsoletion is that this term represents a gene product.
  • [ ] The reason for obsoletion is that this term refers to a class of proteins.
  • [ ] The reason for obsoletion is that this term was added in error.
  • [ ] The reason for obsoletion is that more specific terms were created.
  • [ ] The reason for obsoletion is that this term was an unnecessary grouping term.
  • [x] The reason for obsoletion is that the meaning of the term is ambiguous.
  • [ ] The reason for obsoletion is that is not known to be catalyzed by any gene product.
  • [ ] The reason for obsoletion is that it more specific than the specificity of any known gene product.
  • [x] The reason for obsoletion is that there is no evidence that this function/process/component exists.

• "Replace by" term (ID and label)

No replacement

• "Consider" term(s) (ID and label)

No suggestions for reannotation

• Are there annotations to this term?
• How many EXP:1 from UniProt
• Are there mappings and cross references to this term? (InterPro, Keywords; check QuickGO cross-references section)

No

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

No

• Any other information

Talked to expert (Alex Whitworth) about this term and we agreed that this is not a process - it broadly is trying to capture a whole disparate range of processes that occur in "biogenesis", but this really cannot be sufficiently described by an umbrella term.

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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

[hattrill]

tagging FYI @gantonazzo

[pgaudet]

Dear all,

The proposal has been made to obsolete GO:0140655 mitochondrial proliferation. The reason for obsoletion is that the term is not clearly defined and usage has been inconsistent. There is 1 EXP annotation to this term by UniProt (disputed in P2GO). There are no mappings; this term is not present in any subsets.

You can comment on the ticket: https://github.com/geneontology/go-ontology/issues/26545

Thanks, Pascale