Obsoletion request: cellular metabolic process and regulation of cellular metabolic process terms

[edwong57]

Please provide as much information as you can:

• GO term ID and Label
• GO:0044237 cellular metabolic process
• GO:0046950 cellular ketone body metabolic process
• GO:0046379 extracellular polysaccharide metabolic process
• GO:0031323 regulation of cellular metabolic process
• GO:0006521 regulation of cellular amino acid metabolic process
• GO:0031324 neg regulation of cellular metabolic process
• GO:0031325 pos regulation of cellular metabolic process

The reason for obsoletion is that these terms are redundant terms to:

• GO:0008152 metabolic proces
• GO:1902224 ketone body metabolic process
• GO:0005976 polysaccharide metabolic process
• GO:0019222 regulation of metabolic process
• GO:0006521 regulation of amino acid metabolic process
• GO:0009892 neg reg of metabolic process
• GO:0009893 pos reg of metabolic process

Related to clean up of cellular process terms - https://github.com/geneontology/go-ontology/issues/28908

• "Replace by" term (ID and label) Cellular term annotations should be moved to the corresponding non-cellular terms

• Are there annotations to this term?

• GO:0044237 cellular metabolic process: 41 EXP

• GO:0046950 cellular ketone body metabolic process: 4 EXP

• GO:0046379 extracellular polysaccharide metabolic process: 46 EXP

• GO:0031323 regulation of cellular metabolic process: 6 EXP

• GO:0006521 regulation of cellular amino acid metabolic process: 8 EXP

• GO:0031324 neg regulation of cellular metabolic process: 0 EXP

• GO:0031325 pos regulation of cellular metabolic process: 4 EXP

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

7 mappings/cross refs to review

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

• GO:0044237 cellular metabolic process - in do_not_annotate

• GO:0046950 cellular ketone body metabolic process - in goslim_pir

• GO:0046379 extracellular polysaccharide metabolic process - not in any subset

• GO:0031323 regulation of cellular metabolic process - in do_not_annotate

• GO:0006521 regulation of cellular amino acid metabolic process

• GO:0031324 neg regulation of cellular metabolic process: gocheck_do_not_annotate

• GO:0031325 pos regulation of cellular metabolic process: gocheck_do_not_annotate

• Any other information

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Checklist for ontology editor

Check term usage and metadata in Protégé

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

Check annotations

• [x] 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
• [x] 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
• [x] find external mappings (via IEAS), include in obsoletion notice
• [x] tag curators in Annotation Review ticket. Responsible annotator for each group: https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv

Notification

• [x] create obsoletion announcement
• [x] announce to GO friends (go-friends@mailman.stanford.edu)
• [x] paste the text in the ontology ticket

[deustp01]

Four Reactome pathways fixed as suggested (but is this this suggested term correct? GO:0006521 regulation of amino acid metabolic process)

[edwong57]

Which Reactome pathways are they? What were the annotations?

I think the idea is that since metabolic process has been moved under 'cellular process' that 'regulation of amino acid metabolic process' has 'cellular process' as a parent and there's no need to have a separate 'regulation of cellular amino acid metabolic process' term. So, parentage-wise, I don't think that those should change going from 'regulation of cellular amino acid metabolic process' to 'regulation of amino acid metabolic process,' if that was your concern.

[deustp01]

Which Reactome pathways are they? What were the annotations?

The GO BP terms associated with Reactome pathways R-HSA-1428517 "Aerobic respiration and respiratory electron transport", R-HSA-163675 "ChREBP activates metabolic gene expression", R-HSA-74182 "Ketone body metabolism", and R-HSA-350562 "Regulation of ornithine decarboxylase (ODC)", each needed updating to replace a cellular~ term with a plain metabolism one; no arguments from here about the metabolism versus cellular-metabolism distinction. The failure of the usage survey done as part of a GO obsoletion to pick up these Reactome instances is a known problem due to how we capture the BP terms and export that information in a GAF, that we are slowly working on.

[pgaudet]

Hi @deustp01

The TAS and NAS are now included in the reports. I thought this would result in Reactome's annotations being included in reports. Can you give a specific example of an annotation you expect to be reported that was missing? Looks like we may need to fix something else.

Thanks, Pascale

[deustp01]

Can you give a specific example of an annotation

The three BP-to-pathway annotations in my last comment. @ukemi is the planned cross-referencing of Reactome pathways (rather than reactions) to GO terms relevant / helpful here? I guess that it is but can't explain clearly.

[srengel]

looks like these changes have already been made, but the email said we have until Oct14th.

[edwong57]

The terms listed in this ticket are still showing up in protege and the latest go-edit.obo, so it doesn't look like these have been obsoleted. I didn't tag SGD in the annotation review since the annotations should be replaced automatically with Noctua. I can assign someone, but thought it was unnecessary since it was going to be done computationally.

I did obsolete a few precomposed terms (20919 and 20920) that only had PomBase annotations after those got cleaned up.