Cellular & (non-cellular) metabolic processes

[pgaudet]

Hello,

I am creating a fresh ticket for the work started in https://github.com/geneontology/go-ontology/issues/17904

We have decided that all the chemical metabolic processes are cellular processes, so the following terms need to be fixed.

• if there is a corresponding 'non-cellular' term, the term should be obsoleted and replaced by that 'non-cellular' process term.
• if there is no corresponding 'non-cellular' term, the term label, definition and logical definiton should be fixed to the non-cellular forms.

Also, if there are asserted classes, these should generally be removed, unless they provide information that is not being inferred. Usually the ChEBI hierarchy should infer all parents that are needed.

Metabolic process

• [x] GO:0044237 cellular metabolic process
• [x] GO:0044255 cellular lipid metabolic process
• [x] GO:0043446 cellular alkane metabolic process
• [x] GO:0043449 cellular alkene metabolic process
• [x] GO:0043452 cellular alkyne metabolic process
• [x] GO:0042180 cellular ketone metabolic process
• [x] GO:0006081 cellular aldehyde metabolic process
• [x] GO:0046950 cellular ketone body metabolic process
• [x] GO:0090345 cellular organohalogen metabolic process
• [x] GO:0090346 cellular organofluorine metabolic process
• [x] GO:0052701 cellular modified histidine metabolic process
• [x] GO:0006575 cellular modified amino acid metabolic process
• [x] GO:0046379 extracellular polysaccharide metabolic process
• [x] GO:0031323 regulation of cellular metabolic process
• [x] GO:0010565 regulation of cellular ketone metabolic process
• [x] GO:0006521 regulation of cellular amino acid metabolic process
• [x] GO:0090347 regulation of cellular organohalogen metabolic process
• [x] GO:0090348 regulation of cellular organofluorine metabolic process
• [x] GO:0031324 negative regulation of cellular metabolic process
• [x] GO:0031325 positive regulation of cellular metabolic process
• [x] GO:0045763 negative regulation of cellular amino acid metabolic process
• [x] GO:0010675 obsolete regulation of cellular carbohydrate metabolic process
• [x] GO:0090349 negative regulation of cellular organohalogen metabolic process
• [x] GO:0090350 negative regulation of cellular organofluorine metabolic process
• [x] GO:0043094 cellular metabolic compound salvage

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Biosynthetic process

• [x] GO:0044249 cellular biosynthetic process
• [x] GO:0097384 cellular lipid biosynthetic process
• [x] GO:0052703 cellular modified histidine biosynthetic process
• [x] GO:0042398 cellular modified amino acid biosynthetic process
• [x] GO:0045226 extracellular polysaccharide biosynthetic process
• [x] GO:0031326 regulation of cellular biosynthetic process
• [x] GO:2000282 regulation of cellular amino acid biosynthetic process
• [x] GO:0031327 negative regulation of cellular biosynthetic process
• [x] GO:0031328 positive regulation of cellular biosynthetic process

---

Catabolic process

• [x] GO:0044242 cellular lipid catabolic process
• [x] GO:0042402 cellular biogenic amine catabolic process
• [x] GO:0052702 cellular modified histidine catabolic process
• [x] GO:0042219 cellular modified amino acid catabolic process
• [x] GO:0071999 extracellular polysaccharide catabolic process
• [x] GO:0031329 regulation of cellular catabolic process
• [x] GO:1900419 regulation of cellular alcohol catabolic process
• [x] GO:0031330 negative regulation of cellular catabolic process
• [x] GO:0031331 positive regulation of cellular catabolic process
• [x] GO:1900420 negative regulation of cellular alcohol catabolic process
• [x] GO:1900421 positive regulation of cellular alcohol catabolic process
• [x] GO:0150094 amyloid-beta clearance by cellular catabolic process

Obsolete: precomposed:

• [x] GO:0072000 extracellular polysaccharide catabolic process involved in ascospore release from ascus
• [x] GO:2000777 positive regulation of proteasomal ubiquitin-dependent protein catabolic process involved in cellular response to hypoxia

[cmungall]

Note that this would result in many terms that are clearly cellular moving out of the cellular hierarchy.

In 2019 I proposed a simple solution of placing metabolism under CP. https://github.com/geneontology/go-ontology/issues/17904#issuecomment-549545694

The alternative is to get rid of CP altogether. Having a grouping class that is highly incomplete is confusing.

[pgaudet]

Sounds good. I dont think we want to get rid of cellular process - that's very central to @thomaspd 's BP reorganization.

I moved 'metabolic process' under 'cellular process', see https://github.com/geneontology/go-ontology/issues/28932

Thanks, Pascale

[edwong57]

GO:0044237 cellular metabolic process child terms have been moved GO:0044255 cellular lipid metabolic process child terms have been moved GO:0044242 cellular lipid catabolic process child terms have been moved GO:0097284 cellular lipid biosynthetic process child terms have been moved