A conundrum, cell growth terms

[fypoadmin]

I have a query about cell growth

normal cell growth Definition A cellular process phenotype in which cells grow normally. is a child of viable

But inviable cells are sometimes described as growing normally https://rt.sanger.ac.uk/Ticket/Display.html?id=314234

Gene disruption results in lethal arrest of the cell cycle, but spore germination, cell growth, DNA replication and mitosis are all unaffected.

What do we need to do here? I have a mental block what aspect of growth is normal (growth rate)

Original comment by: ValWood

[fypoadmin]

We decided that no growth = inviable

(as opposed to something more strict, for instance observing lysed cells, or no resumption of growth following some change (for instance to a medium not toxic to the mutant)

I cannot see how an arrested cell can grow, replicate DNA AND go through mitosis...surely then it is not arrested?

You could always annotate to an arrest phenotype + normal phenotype for instance cell cycle arrest in mitotic G2 + normal DNA replication

Original comment by: Antonialock

[fypoadmin]

What they are saying is that growth is normal, the cell grows (i.e increases in size) normally, but then there is a problem with cell cycle progression. I see what they mean (becasue growth and division are separable), but I don't know how we describe this different "aspect" of growth in FYPO...Midori may be able to suggest something

Original comment by: ValWood

[fypoadmin]

ew, this could get ugly. I think we haven't really been conscious of making a distinction between "growth" in the very literal sense of "get bigger", versus "growth" in the sense of carrying on with cell division as well as metabolism so that the population grows.

I suspect I ought to recast a lot of the "growth" terms as a cell population phenotypes. For the chemical sensitivity and resistance phenotypes it should be straightforward, because they can all use GO:0072690 (the vegetative growth term) in the xp defs. But stuff under "cell growth phenotype" is likely to be complicated, because not everything there is vegetative growth phase.

And then there's the question of where viability/inviability fit in, which still feels like a muddle to me ...

ow.

Original comment by: mah11

[fypoadmin]

also see [fission-yeast-phenotype:#692] - those changes should help

Original comment by: mah11

[fypoadmin]

Original comment by: ValWood

[fypoadmin]

Right. I've made a big start on this:

Although I suspect it's a bit ontologically dodgy, I've changed the logical definitions of the existing cell growth terms so that they now refer to population growth -- this seems to fit how the growth terms have been used.

I also changed term names and text defs accordingly.

We can now go in and add any terms for "cell growth" defined as strictly increase in cell size, if and when we need them.

Original comment by: mah11

[fypoadmin]

OK when you are ready I need a term for normal cell growth referring to increase in size, and I will reannotate this https://rt.sanger.ac.uk/Ticket/Display.html?id=314234

Original comment by: ValWood

[fypoadmin]

ok, added normal cell growth FYPO:0002062

defined as size increase

Original comment by: mah11

[fypoadmin]

• labels: --> new ontology term, other ontology change
• assigned_to: Midori Harris

Original comment by: mah11

[fypoadmin]

I'm closing this because I think the work I did before the meetings pretty much takes care of it.

If you spot anything horribly amiss, reopen; if you need any more new terms, a new ticket would be best.

Original comment by: mah11

[fypoadmin]

• status: open --> closed-fixed

Original comment by: mah11

[fypoadmin]

OK, I updated cdc8 in 82154f75e067e7cd to use the new cell growth term. After the next update I will do a query and i might be able to identify others like this one which refer to cell, rather than population growth....

Original comment by: ValWood