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Pathogen-Host Interaction Phenotype Ontology
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NTR: normal growth on fenhexamid #387

Closed CuzickA closed 1 year ago

CuzickA commented 1 year ago

For https://github.com/PHI-base/curation/issues/118

Preferred term label

normal growth on fenhexamid

Synonyms

Textual definition

A growth phenotype which describes the absence of change of individuals or populations after exposure to fenhexamid (i.e. indistinguishable from wild type).

Suggested parent term

chemical phenotype

Note: we might want to extra text to the definition of these 'normal growth...' terms to state that '...(i.e. indistinguishable from wild type, which may be resistant or sensitive to the chemical).

CuzickA commented 1 year ago

Hi @ValWood For the pathogen chemistry phenotypes, Kim would like to curate the WT control strains with 'normal growth on [chemical]'. We need to make it clear that 'normal growth' could be resistant or sensitive to the chemical. I am thinking of adding some additional text (in bold) to these PHIPO term definitions "A growth phenotype which describes the absence of change of individuals or populations after exposure to fenhexamid (i.e. indistinguishable from wild type, which may be resistant or sensitive to the chemical)." Does this seem reasonable to you?

ValWood commented 1 year ago

I'm not sure. In FYPO we have terms normal vegetative growth -- normal vegetative growth on chemical blah (to capture when a chemical does not affect growth)

I don't understand how you can have "normal growth" can be both "resistant or sensitive to the chemical." if it grows more, or less with a chemical the growth isn't normal in this condition?

The phenotype only applies to the specific conditions assayed.

CuzickA commented 1 year ago

Thanks. The difficulty is that different wild type strains can be naturally resistant or sensitive to a chemistry.

CuzickA commented 1 year ago

I've described the problem in https://github.com/PHI-base/curation/issues/118

CuzickA commented 1 year ago

Thinking on this some more I have decided against adding the suggested new text to the definitions.

Kim HK had wanted the WT controls curated but after further discussion today we have agreed that this is not the way to go. The 'normal growth on [chemical]' phenotypes should be reserved for when an altered genotype exhibits the same phenotype as the wild type.

I am closing this ticket as the NTR is no longer needed.

Thanks for your help @ValWood