progress and thought questions

[Sue Rhee]

In general, I agree with your perspective. But we need to be a little more
specific. I have a few questions for clarification.

> XXX To continue, the above example is seemingly very appropriate. Yes, I
> think we do need to provide the depth of information on all nodes so
> that detailed assigning can be done - so we do need to provide lots of

What do you mean by 'detailed assigning'? What data objects are you
talking about and are they known to exist?

> terms. Providing the level of detail which just enables folk to assign
> info. to a very course bin (like 'inflorescence') is surely rather
> inadequate, considering the level of the science i.e. that many users
> are working at a much finer level of granularity. Furthermore, I think

What do you mean by 'the science'? Surely we need to make some decisions
on what subareas of science we are trying to faciliate.

> it is only when we 'sweat' at developing the finer structure now, will
> we encounter & overcome the 'structure difficulties' that are possibly
> lurking. This 'building' is going to be complex/multi-floored... -we

That is true to a certain extent but we need to do this incrementally with
the understanding that the it is a dynamic process and has a very
practical use case (i.e. annotate existing gene expression patterns and
mutant phenotype). The best thing we can do now is to clearly define the
organizing principles and stick to them for consistency. We don't need to
solve all of the nuances in the beginning.

Sue

> need to ensure that we've built the foundation well so that the
> super-structure can be supported. While retrofitting should always be
> possible I urge us all to go deeper now rather than leaving that for
> later. To me this detailed approach is/should be the goal of the
> 'consensus ontology'. Perhaps, as a compromise, we could develop certain
> nodes with fine granularity, based on perceived needs of our potential
> consumers - here I'm assuming that some areas of anatomy are receiving
> much more research attention than other (perhaps a wrong assumption).
> Other nodes, perceived to be 'less needful' of fine granularity could be
> worked on 'later' - but we should advertise that users should voice
> their need for increased granularity wherever such needs are
> encountered.
>
> - Leszek
>
>
> > Elizabeth A. Kellogg
> > Department of Biology
> > University of Missouri-St. Louis
> > 8001 Natural Bridge Road
> > St. Louis, MO 63121
> > phone: 314-516-6217
> > fax: 314-516-6233
> > http://www.umsl.edu/divisions/artscience/biolo> gy/Kellogg/Kellogg/
> >
> >
> >
>

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Sue Rhee                         	rhee at acoma.stanford.edu
The Arabidopsis Information Resource	URL: www.arabidopsis.org
Carnegie Institution of Washington	FAX: +1-650-325-6857
Department of Plant Biology		Tel: +1-650-325-1521 ext. 251
260 Panama St.
Stanford, CA 94305
U.S.A.
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