Growth and development

[Chisholm, Rex FSM]

Dictyostelium is one example where growth and development is
"uncoupled".  In this case the separation is pretty clear as growth
requires nutrients and development occurs when the cells are starved.
The suggestion of having a child of growth that is developmental growth
nicely solves this problem.  I don't feel strongly about the
non-dvelopmental growth term.  I'd probably just use growth, hence I
guess I agree with David.

Rex

-----Original Message-----
From: David Hill [mailto:dph at informatics.jax.org] 
Sent: Wednesday, April 27, 2005 11:17 AM
To: Chris Mungall
Cc: J Clark; development; Chisholm, Rex FSM
Subject: Re: Growth and development

Hi Chris,

I think your solution to make developmental growth is a good one. I'm
not sure we need non-developmental growth. Couldn't we just make sibs of
developmental growth under growth that would be specific for the types
of non-developmental growth.
David


Chris Mungall wrote:

>Thanks Jen - I think you've summed it up well.
>
>Just to reiterate - the ontology should not be constructed around the 
>limitations of any particular tool. However, tools can be useful to 
>pinpoint areas of the ontology where there is a lack of formal rules 
>and consistency.
>
>Does it not seem slightly unsatisfactory to anyone else that one has to

>appeal to some vague intuition that some particular research community 
>may hold to decide where 'x growth' should have an 'x development' 
>parent? It seems that this kind of ad-hoc knowledge is fairly fragile 
>and liable to change at any time, causing flux in the ontology.
>
>Or try thinking about it another way: given adequate resources, would 
>it be possible to partition the cell type ontology into cells which 
>sometimes grow without being part of some developmental program (in 
>non-pathological wildtype scenarios) and those that necessarily entail 
>development when they grow? Does anyone have a sense of whether that 
>partition could be made at a relatively high/generic level in CL, or 
>whether it would be more like a collection of ad-hoc exceptions to the 
>automatically-entails-development rule? How would that partition differ

>if constructed by a different curator? How stable would this partition
be?
>Are there experiments that can be done to justify particular choices in

>constructing the partition?
>
>This partition - if constructed - could be used by either a computer 
>program, or a curator to decide whether x-growth is a child of 
>x-development.
>
>Even if we do not partition CL in this way, it useful to imagine this 
>as a thought experiment. Is such a partition even meaningful?
>
>Here is another, and in my opinion simpler, solution:
>
>Let's imagine we split growth into 'growth', 'developmental growth' and

>'non-developmental growth'. Curators can use their judgement to choose 
>which cross-products to manifest in the ontology (so there would be 
>many more 'x developmental growth' terms than 'x non-developmental
growth'
>terms, I would imagine).
>
>This shifts the question of 'is this instance of growth part-of/is-a 
>development?' to the annotator, where it can be decided on a case by 
>case basis.
>
>This can be either good or bad, depending on whether the imaginary 
>partition discussed above is a constant, unwavering fact of biology or 
>really something that is only true or false on a per experimental 
>observation basis.
>
>Cheers
>Chris
>
>On Mon, 25 Apr 2005, J Clark wrote:
>
>  
>
>>Hi,
>>
>>At the consortium meeting we decided to move 'growth' so that it is a 
>>sibling of 'development' rather than a child.
>>
>>Chris and I were talking about it afterwards and he was asking if 
>>there is a rule that he can use for obol so that he knows when 'x 
>>growth' terms should have an 'x development' parent.
>>
>>For example, is the growth that precedes bacterial division always, 
>>sometimes, or never considered to be part of development?
>>I asked around about this, and the view was that some species research

>>communities think that this kind of growth is part of development and 
>>some think it isn't. Chris was concerned that if species research 
>>communities differed in their view of this then it would be impossible

>>to represent the information in an ontology structure.
>>
>>I am meant to be implementing the changes to the growth terms but I 
>>don't feel I can go ahead with that while Chris has these doubts about

>>the representation of different views of growth in a single DAG.
>>
>>After failing to reach a concensus on this at the meeting I thought it

>>would be best to try to resolve this problem as soon as possible while

>>the discussion is still fresh in our minds. I have written to the key 
>>people in the discussion to make sure they're all free this week 
>>(David, Rex, Tanya, Chris). This e-mail is an attempt to restart that 
>>discussion so that Chris can represent his views directly to the 
>>people involved. I'm hoping that he can get a satisfactory resolution 
>>to his question so I can go ahead and implement the change to the 
>>growth term.
>>
>>Thanks for taking the time to help sort this out. I have attached the 
>>minutes of the growth v. development discussion in case anybody needs 
>>a reminder of what was said.
>>
>>Best wishes,
>>
>>Jennifer
>>
>>
>>
>>
>>    
>>


--
David P. Hill, Ph.D.
Senior Scientific Curator
Gene Expression Database
Gene Ontology Consortium
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, ME 04609-1500
tel:207-288-6430
htpp://www.informatics.jax.org