NTR: Response to chemical phenotype (and re-structure)

[CuzickA]

See #290

[CuzickA]

NTR: Response to chemical phenotype PHIPO:00001218 70f3530

move below under this new term 9649a8e

Next: update definitions

[CuzickA]

also need NTR: normal growth on chemical (@ValWood should we have a term specify each chemical here, or add actual chemical as a condition?)

[ValWood]

We have precomposed these. I think we should add as needed so that the default querying will work. (normal growth on chemical won't make sense on its own as an annotation)

[CuzickA]

edit PHIPO:0001218 response to chemical phenotype -> chemical 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 chemical stimulus. new def A growth phenotype which describes the sensitivity, resistance or absence of change of individuals or populations after exposure to a specific chemical.

PHIPO:0000022 increased resistance to chemical old def A single species population phenotype in which a population shows increased resistance to a chemical stimulus. Resistance to a chemical is usually measured by determining the maximum concentration of the chemical at which a population grows and divides. new def A growth phenotype which describes the resistance of individuals or populations after exposure to a specific chemical. Resistance to a chemical is usually measured by determining the maximum concentration of the chemical at which an individual or population grows and divides.

PHIPO:0000021 increased sensitivity to chemical old def A single species population phenotype in which a population shows decreased resistance to a chemical stimulus. Resistance to a chemical is usually measured by determining the maximum concentration of the chemical at which a population grows and divides. Typically, populations are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type populations to grow. new def A growth phenotype which describes the sensitivity of individuals or populations after exposure to a specific chemical. Typically, individuals or populations are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow.

d8d0a5a

[CuzickA]

add exact synonym 'decreased resistance to chemical' to 'PHIPO:0000021 decreased resistance to chemical' c557754

[CuzickA]

Plan to merge 'increased resistance to chemical' and 'increased resistance to chemical during growth' 'increased sensitivity to chemical' and 'increased sensitivity to chemical during growth'

Need to look up which terms Molecular Connections if using for high level phenotype term and keep these terms as the winning terms.

[CuzickA]

We have precomposed these. I think we should add as needed so that the default querying will work. (normal growth on chemical won't make sense on its own as an annotation)

Will these 'normal growth on chemical X' sit directly under 'chemical phenotype'?

[CuzickA]

There are multiple 'resistance to chemical terms' that need edits to their definitions

Today we mocked up this new definition resistance to 4-aminosalicylic acid A growth phenotype which describes the resistance of individuals or populations after exposure to 4-aminosalicylic acid. Resistance to a chemical is usually measured by determining the maximum concentration of the chemical at which an individual or population grows and divides.

@ValWood please can you confirm that this is correct and then we can ask @jseager7 to bulk update these definitions.

[CuzickA]

Likewise for the 'sensitive to chemical terms'

sensitive to 4-aminosalicylic acid A growth phenotype which describes the sensitivity of individuals or populations after exposure to 4-aminosalicylic acid. Typically, individuals or populations are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow.

@ValWood please check this one too before bulk edit of these terms. Thanks

[ValWood]

On 07/12/2020 16:45, CuzickA wrote:

There are multiple 'resistance to chemical terms' that need edits to their definitions image https://user-images.githubusercontent.com/11753634/101378797-71847000-38ab-11eb-874c-1a6640556edd.png

Today we mocked up this new definition resistance to 4-aminosalicylic acid A growth phenotype which describes the resistance of individuals or populations after exposure to 4-aminosalicylic acid. Resistance to a chemical is usually measured by determining the maximum concentration of the chemical at which an individual or population grows and divides.

@ValWood https://github.com/ValWood please can you confirm that this is correct and then we can ask @jseager7 https://github.com/jseager7 to bulk update these definitions.

I think this is OK... and the corresponding sensitivity term

[CuzickA]

Thanks @ValWood @jseager7 sounds like we can move forward with bulk updating these term definitions when you are ready.

[mah11]

A growth phenotype which describes the resistance of individuals or populations after exposure to 4-aminosalicylic acid. Resistance to a chemical is usually measured by determining the maximum concentration of the chemical at which an individual or population grows and divides.

I think this is OK...

Not quite - this definition does not include anything to indicate that a chemical resistance phenotype would be annotated for a mutant that can grow in a higher concentration of the chemical than wild type. You'll want to change the second sentence to "Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow." or something similar. (Note: I'll edit the corresponding FYPO highllevel defs to match; the chemical-specific terms already have suitable text.)

[jseager7]

@CuzickA Based on the discussion above, this is the template I'm planning to use:

A growth phenotype which describes the resistance of individuals or populations after exposure to [CHEMICAL]. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow.

Is that okay?

[CuzickA]

Thanks @mah11

@jseager7 above seems fine to me for the 'resistance to'

And for the 'sensitive to' we could use

A growth phenotype which describes the sensitivity of individuals or populations after exposure to [CHEMICAL]. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow.

Note to self: may need to update defs on parent terms. DONE

[CuzickA]

Plan to merge 'increased resistance to chemical' and 'increased resistance to chemical during growth' 'increased sensitivity to chemical' and 'increased sensitivity to chemical during growth'

Need to look up which terms Molecular Connections if using for high level phenotype term and keep these terms as the winning terms.

In the slides sent to MC we asked them to map children up to

Therefore, I can merge PHIPO:0000412 'increased resistance to chemical during growth' into PHIPO:0000022 'increased resistance to chemical' DONE 167db3e PHIPO:0000020 'increased sensitivity to chemical during growth' into PHIPO:0000021 'increased sensitivity to chemical' DONE ecf25ec

[CuzickA]

Edit PHIPO:0000021 'increased sensitivity to chemical' def to A growth phenotype which describes the sensitivity of individuals or populations after exposure to a specific chemical. Typically, organisms are deemed sensitive to a chemical if they stop growing (and may die) at a concentration of the chemical that allows wild type individuals or populations to grow.

Edit PHIPO:0000022 'increased resistance to chemical' def to A growth phenotype which describes the resistance of individuals or populations after exposure to a specific chemical. Typically, organisms are deemed resistant to a chemical if they survive at a concentration of the chemical that does not allow wild type individuals or populations to grow.

c071b39

[jseager7]

I've updated all the chemical term definitions to match the new definitions above.

[CuzickA]

Great thanks @jseager7

Closing ticket for now