cell density

[sbello]

Please consider creating a term for cell density. Defined along the lines of 'number of cells per unit area' Please also create increased and decreased children. We currently have 57 MP terms related to changes in tissue cell density for which this term would be used. The definition needs to distinguish this from cell number terms where we used amount.

[nicolevasilevsky]

@sbello and @cmungall do you think an appropriate parent would be PATO_0001019 'mass density'?

[sbello]

Looking at definitions mass density is "A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size." and mass in PATO is "A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter". The question I had was whether cells per unit area is really equivalent to a change in the amount of matter per unit area? You could envision a situation where an organism has more cells per unit area because the cells are smaller but no change in tissue weight, so is that still a change in the amount of matter? I had taken the PATO mass and mass density terms to be referring to the physics concepts of mass and mass density which I don't really think fit this case. We want something more like the definition of population density. But maybe I'm overthinking the whole thing. Or possibly getting tripped up by what is meant by "virtue of some influence is exerted by " which I find confusing.

[nicolevasilevsky]

@sbello I agree, mass density doesn't seem quite right. There is PATO_0002003 'population quality', (def: A quality that inheres in an entire population or part of a population.) Do you think that would work as a parent?

There is also PATO_0001396 'cellular quality', def: A monadic quality of continuant that exists at the cellular level of organisation.
but that doesn't seem quite right either.

[sbello]

I think population quality makes sense since it is a population of cells.
The "monadic quality" part of the cellular quality makes me think that 'cellular quality' is out.

[cmungall]

not sure, also seems quite specific for PATO, can be discussed next week

…

On 2 Aug 2018, at 22:01, Nicole Vasilevsky wrote: @sbello and @cmungall do you think an appropriate parent would be PATO_0001019 'mass density'? -- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: #173 (comment)

[nicolevasilevsky]

We never discussed this when we were together in person. Any thoughts on how to proceed?

[sbello]

Adding this to agenda for Upheno call next week as we're adding more of these terms

[sbello]

cell population density
a quality inhering in a population of cells by virtue of the number of cells per unit area or volume
also add increased and decreased children
discussed on Thursday's UPheno call