Obsoletion request: anaerobic/aerobic fructose catabolic process (GO:0019325/GO:0019576)

[sjm41]

Please provide as much information as you can:

• GO term ID and Label

id: GO:0019325
name: anaerobic fructose catabolic process
def: "The chemical reactions and pathways resulting in the breakdown of fructose that occurs in the absence of oxygen." [GOC:ai]
xref: MetaCyc:ANAEROFRUCAT-PWY
is_a: GO:0006001 ! fructose catabolic process
is_a: GO:0019317 ! fucose catabolic process

id: GO:0019576
name: aerobic fructose catabolic process
def: "The chemical reactions and pathways resulting in the breakdown of fructose that occurs in the presence of oxygen." [GOC:ai]
is_a: GO:0006001 ! fructose catabolic process

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

• The reason for obsoletion is that the term is not clearly defined.
• The reason for obsoletion is that the meaning of the term is ambiguous.

GO:0019325 is based on MetaCyc:ANAEROFRUCAT-PWY, which is "homolactic fermentation" (glucose -> lactate, via pyruvate), and which is already (correctly) an xref on "GO:0019661 glucose catabolic process to lactate via pyruvate"

Also, GO:0019325 has incorrect parent of "fucose catabolic process"

• Are there annotations to this term?
  0 annotations to either term.

• 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
  OK with @deustp01 and @ukemi if we obsolete these two terms? They are sister terms to other fructose catabolic process that are actually used and well-defined:

fructose catabolic process
|__aerobic fructose catabolic process
|__anaerobic fructose catabolic process
|__fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate
|__glycolytic process from fructose through fructose-6-phosphate
|__glycolytic process through fructose-1-phosphate

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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 ([email protected])
• paste the text in the ontology ticket

[deustp01]

Quick sanity check on this and #27616 during the weeds call this Thursday?

[sjm41]

Decision on call (with @deustp01 and @ukemi) was that we should proceed with obsoletion.