Growth and development

[David Hill]

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