Growth and development

David Hill dph at informatics.jax.org
Wed Apr 27 11:25:24 PDT 2005 

Hmmm... Cell development should NOT include the steps involved in 
committing it to a specific fate. This is the distinction between 
differentitation and development. Differentiation includes the processes 
involved in commitment. Development is what the cell does once it knows 
what it is going to be. I don't think we can have the rule between 
growth and development because not all cells that develop grow. Some 
change without any growth.

David






Pascale Gaudet wrote:

>Could a rule be, if there is a "xx cell development", then you could have "xx 
>cell growth"?
>
>With respect to Dicty, I think that would work, since all have cell 
>differentiation but no cell development processes. Maybe that's just because I 
>don't understand the difference between the two?
>
>*/y/ cell differentiation *Processes whereby a relatively unspecialized cell 
>acquires specialized features of a /y/ cell. (N.B. This may be development of 
>/y/ cell type or a set of cells of /y/ cell type. This will involve the change 
>of a cell or set of cells from one cell identity to another.)
>
>*/y/ cell development* Processes aimed at the progression of a /y/ cell over 
>time, from initial commitment of the cell to a specific fate, to the fully 
>functional differentiated cell.
>
>Pascale
>
>At 01:34 PM 4/27/2005 -0400, David Hill wrote:
>
>> I don not think that we should add developmental growth to all the term names, 
>> for the reason you mention.
>>
>> David
>>
>> Tanya Berardini wrote:
>>
>>> Would having the 'developmental growth' term mean that all of its
>>> children would also have the string 'developmental growth' as part of the
>>> term name?  Taking our example from the meeting, 'oocyte growth', would
>>> that now become 'oocyte developmental growth' or not?  If it does, it
>>> think it just looks weird and would not be an intuitive term to search on.
>>> Could this just be a synonym and not the primary term name or would that
>>> mess up OBOL?
>>>
>>> Tanya
>>>
>>>
>>> On Wed, 27 Apr 2005, Chisholm, Rex FSM wrote:
>>>
>>>  
>>>
>>>> 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
>>>>
>>>>
>>>>   
>>>
>>>
>>> -------------------------------------------------------------------------------
>>> Tanya Berardini, Ph.D.                  tberardi at acoma.stanford.edu
>>> The Arabidopsis Information Resource    FAX: (650) 325-6857
>>> Carnegie Institution of Washington      Tel: (650) 325-1521 ext. 325
>>> Department of Plant Biology             URL: http://arabidopsis.org/
>>> 260 Panama St.
>>> Stanford, CA 94305
>>> -------------------------------------------------------------------------------
>>>
>>>  
>>
>>
>>
>> -- 
>> 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
>  
>


-- 
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

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