Growth and development

[Chris Mungall]

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
>
>
>
>