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

[Tanya Berardini]

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