Obsoletion / merge (direct replacement) request: GO:0019659 glucose catabolic process to lactate (fermentation)

[dragon-ai-agent]

Shadow ticket of geneontology/go-ontology#31217

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Please provide as much information as you can:

• GO term ID and Label

1. GO:0019659 glucose catabolic process to lactate =>
   rename "pyruvate fermentation to lactate" only annotation is lactate dehydrognease and fermentation is now confined to post glycolytic pathway

2. GO:0019658 glucose fermentation to lactate and acetate (no annotations)
   This has exact synonym bifid pathway and is a pathway unique to microbiome bacteria
   make term name "bifid shunt"
   make glucose fermentation to lactate and acetate exact synonym
   move directly under fermentation
   add taxon "only in bacteria"

3. obsolete GO:0019656 heterolactic fermentation => direct replace with GO:0019659 now named pyruvate fermentation to lactate

4. obsolete GO:0019661 homolactic fermentation => direct replace with GO:0019659 now named pyruvate fermentation to lactate

(homolactic and heterolactic describe the upstream part of the pathway i.e the source of the lactic acid. Use GO -CAM coupling to capture this)

5. obsolete GO:0019244 lactate biosynthetic process from pyruvate => direct replace with GO:0019659 now named pyruvate fermentation to lactate

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

• 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.

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

All obsolete can be directkly replaced by
GO:0019659 glucose catabolic process to lactate
rename "pyruvate fermentation to lactate"

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

• Are there annotations to this term?

• How many EXP: 1
  automatic reannotation

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

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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

[cmungall]

@dragon-ai-agent please analyze and implement

[dragon-ai-agent]

🤖 Working on it...

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— @dragon-ai-agent

[cmungall]

@dragon-ai-agent please do this again. I closed the first PR as it was accidentally using old agent instructions

[dragon-ai-agent]

🤖 Working on it...

Follow along: View workflow run

— @dragon-ai-agent