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Summary of AFGC Category Feedback and New Topic: Growth Media

David Finkelstein finkel at genome.stanford.edu
Fri Nov 19 14:07:25 EST 1999

Hi Everyone,

Here's a summary of the recent feedback on the AFGC
Categories. Our thanks to all those to have responded, I'm really enjoying
the process and appreciate the serious thought behind your responses.
This is a great way to get a glimpse of the thinking in the plant
field as a whole.  Again I'd like to remind those not devoted solely to
Arabidopsis that your input is valued.  I've been collecting categories
that I think are best applied to crop plants such as maize and soybean.
When they're presentable I'll post these as well.


Some readers strongly favor fewer catgories while others like more
refinements.  I typically receive 3 to 4 times the number of requests
for more categories rather than less.  I recognize that this excercise
expressly encourages more categories and is not a valid sampling survey.
Currently, we are simply collecting as many of your thoughts as possible.


As you will see, including all possible categories suggested for all
experiments will likey be a tremendous burden on each experimenter.
We at AFGC are very open to suggestions about acheiving a middle ground.
Clearly we will have some optional fields. Alternatively, we may consider
optional forms with differing degrees of refinement.  You ideas are welcome.
I don't expect to resolve the lumper/splitter question without
community input.


Several people suggested including a category like: Developemental Stage
from vegetative through reproductive.

Speaking personally, I favor some form of this idea.

Degrees of refinement vary a great deal:

One group proposes a "universal growth staging system" based on phytometer and
"phyllochron" measurements, This system will require some
development for Arabidopsis and I suspect will be ecotype dependent.

Others tell me current listing is "pretty good" as is.


Two important cases:  field grown conditions (yes, it is done for
Arabidopisis I'm told) and changing conditions during growth (i.e. agar
for initial satage followed by soil).  Readers point out that under
changing conditions and field conditions many of the refined categories
cannot be well measured and for these special cases some fields should
be made optional.

Another reader offers the idea that some fields such and temperature
could be input as a range and average rather than a fixed value.

Requests for additional categories include geograhic location of
experimenter (latitude/longitude), seed storage fields, method of
seed imibition and stratification, and time of harvest specified in
relation to circadian rythymns.


Are the current categories sufficient? accurate? Is your favorite method

Once again you can find these categories off the
http://AFGC.stanford.edu/categories.pdf web site, but you'll need Adobe
Acrobat to read and print them.


David Finkelstein, Ph.D.
Post Doc Fellow in Bioinformatics
Carnegie Institution of Washington
Dept. of Plant Biology
260 Panama Street
Stanford, CA 95305

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