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Pathogen-Host Interaction Phenotype Ontology
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NTR: Response to nutrient (and re-structure) #293

Closed CuzickA closed 3 years ago

CuzickA commented 3 years ago

see #290

CuzickA commented 3 years ago

NTR: Response to nutrient phenotype Parent 'single species phenotype' so that it's children can be used to annotate both unicellular and filamentous pathogens. term made PHIPO:00001216 9dc3412

CuzickA commented 3 years ago

Move terms under PHIPO:00001216 Response to nutrient phenotype 54716c9

image

CuzickA commented 3 years ago

Edit PHIPO:0001075 'auxotrophy phenotype' ->auxotrophic growth 2125f9d

Old def A single species population growth phenotype in which a cell requires a particular organic compound, which is not required by a wild-type cell for its growth. Auxotrophy usually results from a cell's inability to synthesize the compound.

new def A single species response to nutrient phenotype in which an individual or a population of organisms requires a particular organic compound, which is not required by a wild-type for its growth. Auxotrophy usually results from a cell's inability to synthesize the compound.

CuzickA commented 3 years ago

update defs for 4 x carbon source terms a341fe8

old def A population growth phenotype in which organism growth is decreased relative to normal in a medium containing palmitic acid as the carbon source.

new def An individual or population growth phenotype in which organism growth is decreased relative to normal in a medium containing palmitic acid as the carbon source.

CuzickA commented 3 years ago

Note for future: may also need 'Prototrophic growth' grouping term and children

Branch currently looks like image

@ValWood can we check through the definitions on Monday please

CuzickA commented 3 years ago

PHIPO:0001216 response to nutrient phenotype -> nutrient phenotype old def A single species phenotype that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nutrient stimulus. new def A growth phenotype which describes the change or absence of change of individuals or populations (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nutrient stimulus.

PHIPO:0001075 auxotrophic growth old def A single species response to nutrient phenotype in which an individual or a population of organisms requires a particular organic compound, which is not required by a wild-type for its growth. Auxotrophy usually results from a cell's inability to synthesize the compound. new def A growth phenotype which describes an individual or a population of organisms which requires a particular organic compound, which is not required by a wild-type for its growth. Auxotrophy usually results from a cell's inability to synthesize the compound.

PHIPO:0001076 growth auxotrophic for lysine old def Auxotrophy in which a cell is unable to synthesize lysine, and therefore requires lysine in the medium for vegetative cell growth. new def A growth phenotype which describes an individual or a population of organisms which requires lysine for growth. Auxotrophy usually results from a cell's inability to synthesize the compound.

decreased population growth on erucic acid carbon source REMOVE 'population' from term label old def A growth phenotype which describes an individual or a population of organisms which requires lysine for growth. Auxotrophy usually results from a cell's inability to synthesize the compound. new def A growth phenotype which describes the decrease in growth of individuals or populations relative to normal in a medium containing erucic acid as the carbon source.

(make same edits for three other carbon source terms)

af7e278

now looks like image