Some population phenotypes are cellular phenotypes

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Fission Yeast Phenotype Ontology

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Some population phenotypes are cellular phenotypes #4179

Open manulera opened 2 years ago

manulera commented 2 years ago

Not sure if some of these are population phenotypes, since they represent the percentage of cells with a given cellular phenotype. Full list below, but some examples:

Penetrance of cells that have the cellular phenotype bipolar growth
- Decreased/ increased bipolar index
- Decreased/increased frequency of apoptosis
- 'decreased monopolar index'
- 'increased number of cells with astral spindle microtubules'
'abolished cell division timing change upon nitrogen source shift' probably should be under FYPO:0006820 ('abnormal cell growth rate')
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ValWood commented 2 years ago

That's weird. The index terms definitely were always sadded as population terms

ValWood commented 2 years ago

I see you are suggesting they should not be.

I think this was decided as a bit of a fudge because it is a population-level phenotype.

https://github.com/pombase/fypo/issues/49

it is the percentage of cells, but the 'index" is an increase/decrease in this percentage (not just the percentage)

manulera commented 2 years ago

Fair enough, I guess I will understand better the difference once I am familiar with logical definitions. In some cases where the same index can be caused by several cellular phenotypes (The septation index is a special could be altered by changes in the assembly/disassembly timing of the septum, or changes in the duration of the cell cycle).

For other cases where the population phenotype is increased occurence of cell phenotype X, I am not sure this is a population phenotype. increased number of cells with astral spindle microtubules is a clear case of this. I assume in this case what we are comparing is cells that are in mitosis, and comparing how often they have those astral microtubules, this phenotype is then more similar to astral microtubules present in decreased numbers, which is a cell phenotype.

manulera commented 2 years ago

In some cases where the same index can be caused by several cellular phenotypes (The septation index is a special could be altered by changes in the assembly/disassembly timing of the septum, or changes in the duration of the cell cycle).

But then I think we should also include these other possible explanations in increased septation index includes_cells_with_phenotype increased duration of septation from #49

manulera commented 2 years ago

In any case, maybe better for me to go through the uPheno materials before discussing this.

ValWood commented 2 years ago

I think I agree about "increased number of cells with blah"

and the nitrogen shift terms https://github.com/pombase/fypo/issues/2508

and even some of the "index" terms were not modelled as population, like: https://github.com/pombase/fypo/issues/2876

For mitotic index the index represent changes in the percentage of cells entering Mitosis. Unfortunately, the discussion was likely mostly in-person, and not recorded in the ticket. https://github.com/pombase/fypo/issues/1452

and a bit more background in this ticket (and linked ones) https://github.com/pombase/fypo/issues/3009 certainly, this one probably needs revisiting https://github.com/pombase/fypo/issues/2236

We have never been completely happy with it!

manulera commented 1 year ago

This could be closed, I think @ValWood