Arabidopsis database needs

Chris Somerville crs at andrew.stanford.edu
Thu Jun 11 21:03:57 EST 1998


As part of an analysis of the current and future needs for public
Arabidopsis (and other plant) database(s), I am writing to request
your advice, comments and concerns about current and future
Arabidopsis (and other plant) databases.  The motivation and scope for
this request is briefly as follows:

Access to the wide range of genetic resources and information
available for Arabidopsis is currently provided through a range of
electronic databases that can be located by starting a web search at
the AtDB web page maintained by Mike Cherry, Dave Flanders and
colleagues.  Rapid progress toward complete genome sequencing, the
pending proliferation of DNA microarray capabilities and many other
developments are expected to greatly increase the magnitude and
complexity of information that will be available. Therefore it seems
an appropriate time to evaluate what kind of information resources
will allow us (the plant biology community) to most efficiently
utilize the vast amount of information that is accumulating for
Arabidopsis (and other plants).

In 1993 the Arabidopsis steering committee and a group of consultants
produced a report for NSF that identified the Arabidopsis database
needs envisioned at that time.  On behalf of the steering committee
and NSF, I have organized a similar small workshop which will be held
in Madison on June 28 to reevaluate the current and future needs and
to prepare a new report for NSF. Since the goal of the workshop is to
identify current and future needs and opportunities, I invite everyone
to send me comments  and suggestions before June 24 on the following
discussion topics or any related issues.  I would be particularly
interested in receiving some "visionary" ideas about what such
databases could look like in the year 2008 so that we know what to aim
for.  I will collate the response, present it to the participants at
the workshop and post it to the newsgroup.  The report from the
workshop will also be posted to the newsgroup for comments before it
is finalized.  When the needs of the community have been identified,
there will be a second small workshop involving primarily colleagues
with technical expertise in database design and implementation who
will provide additional input on how to achieve the goals identified
by the community.

Here are some of the issues to be discussed at the June 28th workshop:


What should be in the Arabidopsis database and what is a reasonable
time frame for achieving coverage of various types of information?

Who should curate the database(s)? How should information be
collected?

What should the goals be with respect to obtaining data from journals
at the time of publication? (ie., should we ask the journals to
implement a database accession requirement similar to the Genbank
requirement)

Who should "own" the Arabidopsis (or other species) databases, and how
should management and advisory committees be selected and appointed?

Is it feasible and desirable to build one database structure that will
meet the needs for all plants? How can information on other species be
most easily linked to the Arabidopsis database?

How can the database be made financially self-supporting? (i.e., we
cannot depend on continued federal support for such activities)

Is it desirable to have one database or many?

What problems do you currently encounter with access to information?
How could these problems be solved?

I look forward to receiving your comments.
Thanks, Chris Somerville




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