Growth and development

[David Hill]

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