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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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zinc starvation/zinc replete #17973

Open ValWood opened 4 years ago

ValWood commented 4 years ago

we have cellular response to zinc and cellualr response to zinc starvation

https://user-images.githubusercontent.com/7359272/66235533-217aae00-e6e8-11e9-88b7-ce88fc253505.jpg

  1. These could be connected under "cellular response to nutrient"
  2. I think (or at least have used) cellular response to zinc to refer to zinc excess/replete (i.e is defined as zinc stimulus)m. If this is the case can the term be renamed? If this is a general term, can the starvation term be housed underneath it and a descendent created for 'replete'?
raymond91125 commented 2 years ago

It appears that cellular response to [ion] and cellular response to [ion] starvation usually follow distinct paths. (the graph labels are truncated for the 3 highlighted nodes to the left. They are starvation terms) image

raymond91125 commented 2 years ago
  1. Thus the general question is whether 'response to the lack of X' should be subsumed under 'response to X'.
  2. Then we perhaps should review the hierarchy for metal ions to perhaps pare things down. I think everything perhaps should be under homeostasis.
  3. I am not sure if it's a good idea to place these under the nutrient branch as metals can be nutrients and poisons.
pgaudet commented 2 years ago

I am not sure if it's a good idea to place these under the nutrient branch as metals can be nutrients and poisons.

Agreed.

ValWood commented 2 years ago

In this case, should we consider removing the concept of 'nutrient' as a 'role' (similarly to 'drug' and 'cofactor'). Currently the graph is difficult to navigate because terms are separated. Starvation terms are under nutrient and replete terms are not.