Growth and development

[Chisholm, Rex FSM]

I agree.  Besides we don't necessarily do something similar in all other
sections of the graph.

rex 

-----Original Message-----
From: Tanya Berardini [mailto:tberardi at acoma.Stanford.EDU] 
Sent: Wednesday, April 27, 2005 12:50 PM
To: David Hill
Cc: Chisholm, Rex FSM; Chris Mungall; J Clark; development
Subject: Re: Growth and development

Exactly.  That would be my only reservation about implementing the term
'developmental growth' and all that that implies.

Tanya


On Wed, 27 Apr 2005, 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
>

------------------------------------------------------------------------
-------
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
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