[go] Re: regulation of cell cycle vs. regulation of progression through cell cycle

[Valerie Wood]

Hi Tanya,

Sorry for the delay.

At first glance, I think that what you propsed is OK. You are correct 
that the seperate terms were created to cope with the switching between 
mitotic and meiotic cell-cycles, but your solution of making these 
positive and negative regulatory terms respectively seems logically 
consistant.

I think however, there is a more fundamental problem in this portion of 
the graph in that there is some confusion between  the concurrent use of 
meiosis to describe 'meiotic division' and meiosis as a 'developmental 
stage'

I'm not sure if the terms created to cope with the switching between 
mitotic and meiotic cell-cycles rather refer to a switch between 
developmental stage
for example "entry into meiosis" for yeast would include response to 
pheromone, and conjugation etc, and gene products annotated to these 
terms would not necessarily be considered be a 'cell-cycle ' genes.

current child terms of "meiosis"  also include
megasporogenesis (synonym megaspore development ) and these terms do not 
appear to be referring specifically to meiosis as a cell cycle process.

This is essentially what I was trying to describe in
SF 1831804 ] yeast meiotic development.

Even some of the definitions of these terms seem to merge both concepts 
into a single term.

It might make sense to tackle both issues at the same time. I'm not sure 
what the solution is....

Val




Tanya Berardini wrote:

> Dear GO Consortium,
>
> As part of the 'regulates' project, we have come across a set of terms
> in the cell cycle portion of the graph that seem problematic. We are
> writing because we know that a lot of previous work has gone into this
> part of the graph and want to be sure that our plan makes sense. We have
> two sets of terms similar to these:
>
> term: regulation of cell cycle (simple term)
> def:A cell cycle process that modulates the rate, extent or mode of the
> cell cycle.
>
> term: regulation of progression through cell cycle (progression term)
> def: Any process that modulates the rate or extent of progression
> through the cell cycle.
>
> Our question is how does 'regulation of progression through cell cycle'
> differ from 'regulation of cell cycle'?
>
> Note that 'cell cycle' itself is defined as "the progression of 
> ...phases and events ...", implying that regulation of the cell cycle 
> is regulation of progression through the cycle; the same holds for the 
> types of cell cycle (i.e. its is_a children).
>
> cell cycle: The progression of biochemical and morphological phases and
> events that occur in a cell during successive cell replication or
> nuclear replication events. Canonically, the cell cycle comprises the
> replication and segregation of genetic material followed by the division
> of the cell, but in endocycles or syncytial cells nuclear replication or
> nuclear division may not be followed by cell division.
>
> If they are indeed describing the same processes, the 'regulation of %'
> and 'regulation of progression of %' terms should be merged. If not,
> then we need to create a bona-fide biological process called
> 'progression through cell cycle' and we need to differentiate that from
> 'cell cycle' with a really good definition. Currently the progression
> terms are only used in conjunction with regulation.
>
> The way we represent these in the graph is also inconsistent. An example
> follows:
>
> Case 1: No direct link between the 'regulation of progression through
> cell cycle' term and 'cell cycle' term exists.
>
> regulation of cell cycle
> --[i]regulation of progression through cell cycle
>
>
> Case 2: Direct link between 'regulation of progression through meiotic
> cell cycle' and 'meiotic cell cycle' exists.
>
> regulation of meiotic cell cycle
> --[i]regulation of progression through meiotic cell cycle
>
> meiotic cell cycle
> --[p]regulation of progression through meiotic cell cycle
>
>
> We propose:
>
> 1) Merging the 'regulation of progression through' terms
> with their simpler parents when they exist.
>
> 2) Renaming the 'regulation of progression through' terms to their
> simpler forms when the simpler parents do not exist since the parent
> non-regulates terms are already defined as the progression of...
>
> 3) Moving 'cell cycle switching, meiotic to mitotic cell cycle' to
> become an is_a 'negative regulation of meiotic cell cycle' and an is_a
> 'positive regulation of mitotic cell cycle'.
>
> 4) Moving 'cell cycle switching, mitotic to meiotic cell cycle'
> to be an is_a 'positive regulation of meiotic cell cycle' and an is_a
> 'negative regulation of mitotic cell cycle'. We think that the last two
> terms were why 'regulation of cell cycle' and 'regulation of 
> progression through cell cycle' were originally created as distinct 
> terms. However, the movement of these as in 3 and 4 makes more logical 
> sense since the process they describe stops (negatively regulates) one 
> type of cell cycle and initiates (positively regulates)
> another.
>
> Please comment if you think that these merges/renames are not ok.  If 
> this is the case then we will need to make the missing 'progression' 
> terms or 'simpler terms' and will need help in differentiating the 
> 'progression' terms from their parents.
>
>
> David & Tanya
>
>
>
>



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