Defining Growth Conditions

J-Antoni Rafalski J-Antoni.Rafalski at USA.dupont.com
Wed Nov 10 13:36:38 EST 1999


I am a bit concerned that the approach taken seems to create more and more
narrow categories that would be relevant to only very few users and will be
empty in most data base records. Moreover, there will always be categories
and conditions that remain undefined. I would favor defining the most
common and fundamental categories (species, tissue, etc) as indexed fields,
and then relegate the minor categories to a text field called
"description", or whatever. This is the appraoach we (=Stan Luck) are
taking.
Antoni Rafalski
DuPont AgBiotech Genomics





David Finkelstein <finkel at genome.stanford.edu> on 11/09/99 12:58:07 PM

To:   arabidopsis newsgroup <arab-gen at net.bio.net>
cc:   plantarrays at fafner.Stanford.EDU (bcc: J-Antoni Rafalski/AE/DuPont)
Subject:  Defining Growth Conditions




Hi Again Everyone,
     I've gotten really helpful feedback on the age question,
so thanks again for the great input.  I haven't yet updated the
posted list (http://AFGC.stanford.edu/categories.pdf) to reflect
the changes, but I will soon.  I will also post an edited summary of
feedback, without names as requested.
Today, I'd like to tackle a slightly larger question: defining growth
conditions.  For the sake of simplicity these categories only refer to
environmental/biophysical conditions, not to soil, growth media or
fertilizer questions. We'll get there later.
Currently (and subject to change and comment) we will require:
Temperature (day and night)
Day length (duration in hrs. and category (sd, ld, etc.))
Relative humidity-for both day and night
Light intensity (microEinsteins per meter squared per second)
Wavelength range
Light Source (flourescent, incandescent, both, natural etc.)
Growth Room/Chamber (greenhouse, environmental chamber, etc.)
What do you think? Is it enough? too much?
we very much appreciate your opinion.
Just to remind y'all why I'm sending these questions:
 Our goal is a structured list of information that we can design into our
 microarray database that will describe plant experiments.  At the moment
we
 are dealing with the genetic and environmental conditions of the plants
 used as source of probe.
 We are also encouraged by the number of other groups that are interested
 in working together to design a common system.
Regards,
  David
 David Finkelstein, Ph.D.
 Post-doc in Bioinformatics
 Carnegie Institute of Washington
 Stanford, CA 94305

P.S. Any alternative names for these "categories" are welcome.
P.P.S. Any general commentary and criticisms are also welcome. Please
don't feel inhibited if Arabidopsis is not your main interest.

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