Response to phosphate/ nutrient homeostasis

[ValWood]

Please provide as much information as you can:

• Suggested term label:

response to phosphate

• Definition (free text)

Standard def

*** Processes can also be mentioned in the definition.

• Reference, in format PMID:#######

ght5 here https://www.pombase.org/reference/PMID:34028542

others https://www.pombase.org/reference/PMID:37949217 https://www.pombase.org/reference/PMID:26264592 https://www.pombase.org/reference/PMID:31276588 many others

• Gene product name and ID to be annotated to this term

many

• Parent term(s) is_a [GO:0032991 protein-containing complex, or a more specific term], part_of [subcellular location] (if appropriate) capable_of MF (if appropriate) capable_of_part_of BP (if appropriate)

• Any other information

We have GO:0016036 JSON cellular response to phosphate starvation for derivation but not use "response to phosphate" for replete conditions. We need both for essential nutrients otherwise it isn't possible to model the switches in GO-CAMs

(i.e for glucose we have both glucose and glucose starvation)

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proposed parent: relationships: is_a [complex parent], part_of [subcellular location], capable_of MF, capable_of_part_of BP Synonym(s):

[pgaudet]

Is 'response to' that the best way to describe 'replete' conditions? I have been wonderiing if we could describe this more precisely.

[ValWood]

Open to suggestions! I haven't come up with a better way, but we really need to be able to do it.

[pgaudet]

It looks like phosphate homeostasis - maybe 'phosphate homeostasis under phosphate replete conditions'? (a bit of a mouth full though)

[ValWood]

It is more accurate so would we also have 'phosphate homeostasis under phosphate deprivation'?

and would we obsolete the corresponding "response to" terms (these are what I have been using)

[pgaudet]

'phosphate homeostasis under phosphate deprivation'?

This should be the new term names for response to starvation and children; what do you think ?

[ValWood]

I think so. So maybe the parent could be nutrient homeostasis -homeostasis under nutrient deprivation

we would need x homeostasis for each nutrient to group the deprivation and replete I like deprivation rather than starvation, because 'starvation' might imply complete withdrawal of nutrient when its really just a reduction to below some threshold)- probably deprivation conveys this better?

[ValWood]

See https://github.com/geneontology/go-ontology/issues/22996 There is a difference in the programmed response between "nutrient stress" (partial reduction" and total starvation.

[ValWood]

When we address this, we also need to consider this ticket: https://github.com/geneontology/go-ontology/issues/20825