GO:0061387 regulation of extent of cell growth (please refine definition)

ValWood commented 4 years ago

GO:0061387 regulation of extent of cell growth Is defined as : Any process that modulates the extent of cell growth.

What do we mean by this term? Is this term synonymous with "regulation of cell size at cell-division" (as oppose to osmotic size increase and the like) If so "cell division" should be a part of the description The "extent of cell growth" is a result of the coordination between growth and division.

The sibling is GO:0060305 regulation of cell diameter Any process that modulates the diameter of a cell, the length of a line segment that crosses through the center of a circular section through a cell.

but regulating the diameter does not necessarily regulate the size? A cell can be the same overall size but have a change in diameter.

The definitions in this branch are currently a bit circular. Should the definitions mention dimension (or even volume since we are talking about a 3D object?)

You can be a stubby cell, the same size but a different shape

ValWood commented 4 years ago

I see that regulation of cell growth has children like "regulation of axon extension" so I will close this and request the more specific term that I require.

ValWood commented 4 years ago

Actually I will keep it open. I can't compose the new terms because I'm not completely sure about their placement based on the definitions of the existing terms.

regulation of cell size is probably sufficient but I need to be sure that this would be used exclusively for regulating cell size at division and I'm not sur if this is the case based on the descendants.

(isn't regulation of axon extension about growth not size?)

pgaudet commented 3 years ago

@ukemi or @mah11 Do you know anything about the history of those terms ?

GO:0061387 regulation of extent of cell growth has a single direct annotation, it could be merged up, it's not such a useful grouping term (it's grouping processes that are not especially related:
- GO:0030516 regulation of axon extension
- GO:0001559 regulation of cell growth by detection of nuclear:cytoplasmic ratio
- GO:0048670 regulation of collateral sprouting
- GO:0048686 regulation of sprouting of injured axon
GO:0060305 regulation of cell diameter has 4 EXP, 2 from pombase that actually mention diameter - do you think this can be rehoused ? Maybe 'GO:0008361 regulation of cell size' is sufficient ?

There is also one TAIR and one BHF annotation @tberardini @RLovering

@ValWood Please let me know what you'd like to do with those terms.

Thanks, Pascale

mah11 commented 3 years ago

What I know of the history is in #8713, #8856, and #15463. Of the content of those tickets, this comment seems particularly relevant to the first question in the original ticket summary here.

I doubt that it could hurt to edit text definitions to make clearer distinctions between length, diameter, volume, etc.

ValWood commented 3 years ago

I was going to ask @mah11 and @ukemi because I know I keep getting confused here. But I don't think the terms are very clear.

In fact, I am wondering why there are so many EXP annotations (over 1000 annotations) to 'regulation of cell size' , when so little is known about how cell size is controlled, and most of this work has been done in fission yeast (and most quite recently).

I want the term which precisely means "control of cell size" in how big a cell is at division. However, lots of the children of "regulation of cell size" have nothing to do with this, so I don't really know which term to use.

There still appears to be some conflation of "growth" and "regulation of cell size" that I have never been able to unravel.

Note that the size a call grows to (larger or smaller than normal) is not an indicator of a cell size regulator, because cells change size for a number of reasons. They can get bigger if division is blocked but growth continues, or during diploidization. However "regulation of cell size" seems to be used fairly ubiquitously for all sorts of things.....

ValWood commented 3 years ago

so here is a problem for example:

under "regulation of cell size" is GO:0061387 regulation of extent of cell growth Definition: Any process that modulates the extent of cell growth.

Which seems OK, BUT the descendants of GO:0061387 include GO:0030516 regulation of axon extension Any process that modulates the rate, direction or extent of axon extension.

This definition is broader than the parent , not narrower. It introduces "rate" and "direction"

mah11 commented 3 years ago

I want the term which precisely means "control of cell size" in how big a cell is at division.

Buried in the saga that is ticket #13000 are a couple of comments where I asked whether this phenomenon is really regulation of cell growth, as opposed to regulating cell division (via regulating one or more cell cycle phase transitions) so that it occurs at a certain cell size. From this perspective, cell size is what's monitored, but a term describing the regulation would fit in the cell cycle regulation branch.

However, lots of the children of "regulation of cell size" have nothing to do with this, ... the descendants of GO:0061387 include GO:0030516 regulation of axon extension

I agree that some of the is_a GO:0061387 links look wrong (I wonder if they were mistakenly moved from being directly is_a GO:0001558 but I don't remember).

Errors aside, though, there's also the issue of regulating the size of non-dividing cells, which is a lot more important for multicellular organisms than for yeasts, and may well involve regulating growth (but probably not exclusively).

tberardini commented 3 years ago

@pgaudet The Arabidopsis annotation is from UniProt. I'm not sure who to tag to look into it and transfer to another more appropriate term.

pgaudet commented 3 years ago

@ValWood If I merge 'regulation of extent of cell growth' into 'regulation of cell growth' does this address the issues ?

Note that 'regulation of extent of cell growth' has the following children (but I dont think moving them under 'regulation of cell growth is a problem?)

'negative regulation of axon extension involved in axon guidance' 'negative regulation of axon extension involved in regeneration' 'negative regulation of axon extension' 'negative regulation of collateral sprouting in absence of injury' 'negative regulation of collateral sprouting of injured axon' 'negative regulation of collateral sprouting of intact axon in response to injury' 'negative regulation of collateral sprouting' 'negative regulation of formation of growth cone in injured axon' 'negative regulation of sprouting of injured axon' 'positive regulation of axon extension involved in axon guidance' 'positive regulation of axon extension involved in regeneration' 'positive regulation of axon extension' 'positive regulation of collateral sprouting in absence of injury' 'positive regulation of collateral sprouting of injured axon' 'positive regulation of collateral sprouting of intact axon in response to injury' 'positive regulation of collateral sprouting' 'positive regulation of formation of growth cone in injured axon' 'positive regulation of sprouting of injured axon' 'regulation of axon extension involved in axon guidance' 'regulation of axon extension involved in regeneration' 'regulation of axon extension' 'regulation of collateral sprouting in absence of injury' 'regulation of collateral sprouting of injured axon' 'regulation of collateral sprouting of intact axon in response to injury' 'regulation of collateral sprouting' 'regulation of formation of growth cone in injured axon' 'regulation of sprouting of injured axon'

Thanks, Pascale

ValWood commented 3 years ago

Looking at it maybe we should not tinker with this branch. It should pro bably be addressed with logical definitions from the top down at some point because there is a very mixed bag of stuff under here. Growth of populations (in development), directional growth, size increases and more. All seem to be a bit mixed up. Also without annotation guidance almost anything could be annotated to growth, at least in yeast, so we need to be precise whether we mean 'control of size increases'. (i.e the signalling), or any processes which contribute (transport, metabolism, translation, energy production etc)

Perhaps close this for now?

pgaudet commented 3 years ago

OK, but I dont think the merge I propose : 'regulation of extent of cell growth (1 EXP)' into 'regulation of cell growth' would cause problems ? (and it would simplify slightly... )

Please close if you dont think that's useful.

mah11 commented 3 years ago

if I merge 'regulation of extent of cell growth' into 'regulation of cell growth' does this address the issues ?

I strongly recommend against this merge, because 'regulation of extent of cell growth' is narrower than, not identical to, 'regulation of cell growth'. As noted at greater length in the tickets I linked above, regulating extent of growth is only one of several ways that growth can be regulated (rate or direction can also be regulated), i.e. there's a genuine biological difference between 'regulation of extent of cell growth' and its siblings.

Merging also won't solve any problems. Instead:

The text definition of 'regulation of extent of cell growth' itself is pretty sketchy, so it would help to improve it. The distinctive feature this term is meant to capture is control of how much a cell grows (how much additional matter it adds to itself) before stopping.
As Val noted, some of the terms currently under 'regulation of extent of cell growth' may not belong there, but correcting that entails either moving terms or correcting their text definitions, and, yes, adding logical definitions wherever possible.
I have become convinced that the main problem we have specifically for fission yeast is one of annotation, not the ontology. We may simply not have any use for 'regulation of extent of cell growth'; it seems more useful for multicellular organisms in which cells may (for example) grow to a certain extent before or as part of terminally differentiating. (I think we should annotate the pombe cell size at division stuff as regulation of cell division.)

ValWood commented 3 years ago

OK, I see now this is not a term we would use. So a taxon restriction for yeast (which divide at a fixed size) but not for filamentous fungi (which grow top a larger extent with more nutrients), would also be useful.

ValWood commented 3 years ago

Maybe the definition should say Any process that modulates the extent of cell growth of a differentiated cell? (so this process will only refer to non-vegetatively growing cells)

The descendants probably fit this, although I have no idea what a "collateral" is...

ValWood commented 3 years ago

GO:0048668 collateral sprouting -> axon collateral sprouting? (but this isn't a growth term is it? it's structure formation? )

mah11 commented 3 years ago

Maybe the definition should say Any process that modulates the extent of cell growth of a differentiated cell?

I don't know enough to be sure that growth-extent regulation would only apply to cells that have already differentiated, but it may be OK if the scope is extended to diffentiated or differentiating cells ... best check with people who know more, though (maybe @ukemi?).

(so this process will only refer to non-vegetatively growing cells)

I'm not sure I understand this bit.

... although I have no idea what a "collateral" is...

Good thing there's a GO CC term that explains it (GO:0044303) ;)

GO:0048668 collateral sprouting -> axon collateral sprouting?

Yes, the parentage and text def are consistent with this suggestion.

(but this isn't a growth term is it? it's structure formation? )

I don't really know enough about neuron growth, morphogenesis, etc. to have the definitive word on this, but IIRC collaterals and other types of extension form as axons grow directionally -- all that axon growth stuff seems to involve regulating both extent and direction of growth and I'm not the one to try to tease it apart.

ValWood commented 3 years ago

non-vegetatively growing cells -> I mean non-cycling cells

geneontology / go-ontology

GO:0061387 regulation of extent of cell growth (please refine definition) #19737