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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Clarify definition of nitrogen cycle metabolic process, move out urea cycle #27220

Open cmungall opened 8 months ago

cmungall commented 8 months ago

The definition of GO:0071941 nitrogen cycle metabolic process is "The nitrogen cycle is a series of metabolic pathways by which nitrogen is converted between various forms and redox states; it encompasses pathways in which nitrogen is acted upon directly, such as nitrification, denitrification, nitrogen fixation, and mineralization. PMID:16675690"

Is this intended to apply potentially to all taxa or to be restricted to prokaryotes and plants? Does the clause "in which nitrogen is acted upon directly" apply to all nitrogen cycle processes, or is it an optional label for some of them? If the former (all), then urea cycle is out of place because it does not involve conversion of nitrogen the element to anything. If the latter (optional), should purine catabolism to uric acid be added as a sibling of urea cycle, as playing a role in birds and reptiles like the one for urea cycle in mammals?

Originally posted by @deustp01 in https://github.com/geneontology/go-ontology/issues/27217#issuecomment-1983533164

cmungall commented 8 months ago

I agree. The definition references https://en.wikipedia.org/wiki/Nitrogen_cycle which is clearly about the environmental nitrogen cycle

Additionally there are 3 direct annotations, this is too broad a term to directly annotate to

image

One is from CACAO https://amigo.geneontology.org/amigo/reference/PMID:10227138

Two are from PomBase with IC - @ValWood I'm not sure I understand these.

I suggest

  1. remove urea cycle as @deustp01 suggests
  2. clarify definition to be the "standard" cycle
  3. add do_not_annotate
  4. obsolete the 3 regulation terms

Alternatively the term could be obsoleted altogether as being out of scope, we could import ENVO and have the conventional N cycle terms be part-of the ENVO environmental process -- but it's not worth importing a new ontology just for one term, even if this is correct

ValWood commented 8 months ago

Note to self nitrogen cycle metabolic process is in the pombe, and the generic slim but as I'm aware it is only to capture "urea metabolic process" (at least for fungi and metazoa) so we should probably switch to this term instead @pgaudet ? https://www.pombase.org/term/GO:0071941

ValWood commented 8 months ago

Two are from PomBase with IC - @ValWood I'm not sure I understand these.

removed

ValWood commented 8 months ago

See comment here https://github.com/geneontology/go-ontology/issues/27217#issuecomment-1985258770

Maybe we can move away from a generic terms to group nitrogen derivatives because they aren't very precise, and move towards ammonium/ammonia utilization/detoxification with "nitrogen" as related synonyms

That was the NH4.