fwd: Arabidopsis database needs

Chris Somerville crs at andrew.stanford.edu
Mon Jun 15 08:59:24 EST 1998


Forwarded to bionet.maize  by: "Dave Matthews"
<matthews at greengenes.cit.cornell.edu>

> From: "Chris Somerville" <crs at andrew.stanford.edu>
> Newsgroups: bionet.genome.arabidopsis
> Subject: Arabidopsis database needs
> Date: 11 Jun 1998 19:03:57 -0700
>
> 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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