Arabidopsis databases

Randall L Scholl rscholl at magnus.acs.ohio-state.edu
Sat Nov 2 12:58:22 EST 1991




     We thank Richard Cooke for his recent inquiry
on this news service about the two Arabidopsis
databases currently being developed. Since many
newsgroup subscribers may not be completely
familiar with the current status of Arabidopsis
database development, we will take this opportunity
to provide an update.  Several relevant subjects
are addressed below:

1. RELATIONSHIP BETWEEN THE TWO DATABASE PROJECTS       

     It is correct that two independently funded
databases are currently being developed for
Arabidopsis - one associated with the Arabidopsis
Biological Resource Center (called AIMS for
Arabidopsis Information Management System) and the
one of Sam Cartinhour, Mike Cherry, Howard Goodman
and Brian Hauge at MGH (called AATDB for An
Arabidopsis thaliana Database). AIMS is funded by
NSF. It is an on-line service.  AATDB is funded by
the USDA. It will be distributed as magnetic medium
for local use on Sun-type work stations or
Macintosh computers.

     Although these databases will have overlap,
the underlying reasons for their existence are
different, and this will likely be reflected in
composition. The primary objective of AIMS is to
serve the Resource Center for stock information and
ordering. AATDB has a major task of organizing the
large cosmid contig collections and relating these
to other Arabidopsis genetic features. 

2. THE GENERAL DESIGN OF AIMS

     The concept of the AIMS database was developed
as part of our initial proposal for the Arabidopsis
stock center.  We recognized that the maintenance
and distribution of stock information could best be
achieved utilizing electronic means.  It was also
clear that additional information relating to
Arabidopsis could readily be incorporated into such
a system and would complement the basic stock
information.  Thus a comprehensive Arabidopsis
database was proposed.

     The information expected to be included in
AIMS will consist of comprehensive data about
stocks, stock ordering capability, a bibliography
of Arabidopsis possibly including abstracts, a list
of Arabidopsis researchers, current recombination
and physical maps, and possibly DNA sequence
information.  

     To arrive at the best possible design, we plan
to involve the community throughout the database
development process, the first step of which is the
current survey questionnaire.

     While several means of organizing data are
available, we have chosen to utilize an on-line
system.  A Sun computer to be housed at Michigan
State (and maintained by Dr. Pramanik and staff)
and Sybase database software are being purchased. 
Sybase is used by other genomic database projects
such as GenBank.  This combination allows the
construction of a truly relational database and
remote, multiple user access.  Hence, it should be
possible for numbers of individuals  to access the
system simultaneously, and all information will be
interconnected so that maximum information can be
extracted from the stored data.

     The user interface methods of this system will
be varied to allow for different capabilities of 
local terminals.  For on-line use by either telnet
or direct dial-up, multiple window (X-window) or
menu based access will be available.  For modem
access, menu or ftp modes will be possible. In this
way, sophisticated display methods and inquiry
approaches will be possible for individual with
appropriate computers, and basic access and
information will be available to users with less
elaborate computer facilities.  

     We plan to offer a basic version of the system
in spring 1992 and the full version in
approximately one year. 

     
3. SURVEY QUESTIONNAIRES AND THE COORDINATION OF
     DEVELOPMENTAL ACTIVITIES

     We have just mailed a survey questionnaire to  
a number of individuals in the Arabidopsis
community. This survey, which was also distributed
at the ISPMB meetings, represents a comprehensive
treatment of database issues. Although authored at
MSU and OSU, it is designed to serve the
development of both AIMS and AATDB. In fact, the
MGH group had direct input into its development.
The previous survey, authored by the MGH group, was
distributed by e-mail and dealt primarily with user
interface issues.  

     Thus the Arabidopsis database developmental
activities are being coordinated between the two
groups, and ALL INFORMATION GENERATED WILL BE
SHARED.  

     Because we are still developing our mailing
list and the cost of production is high, the AIMS
survey was not distributed to all possible
individuals.  IF YOU DID NOT RECEIVE A SURVEY AT
THE ISPMB MEETINGS OR THROUGH THE MAIL AND WOULD
LIKE TO PARTICIPATE, NOTIFY US AS SOON AS POSSIBLE
BY E-MAIL OR REGULAR MAIL, AND WE WILL BE HAPPY TO
SEND A SURVEY TO YOU.  We aim to achieve the
highest possible degree of community participation
in the development of the AIMS database.

     It is important to note at this juncture that
we will be involving the Arabidopsis community
throughout the AIMS developmental process.  If you
are interested in this subject and desire to
participate, WATCH THIS NEWSGROUP FOR BRIEFINGS. We
will also be communicating by direct mail.

     
4. OVERALL COORDINATION OF ACTIVITIES BETWEEN THE
     TWO DATABASE GROUPS
     
     We are coordinating our efforts at all 
possible levels.  The coordination of the survey
effort has already been described. DATA SUBMITTED
TO EITHER GROUP WILL BE FULLY SHARED:  This
obviously is a very important principle, since
duplicated submissions must be avoided. We are also
sharing information regarding database structuring
so that these features can be as compatible as
possible.

     BE ASSURED THAT OUR TWO GROUPS ARE
COMMUNICATING AND COOPERATING AS FULLY AS POSSIBLE
TO SERVE THE ARABIDOPSIS COMMUNITY.

5. FUTURE PLANS FOR AIMS

     Our database activities are currently funded
for a five-year period, as is the stock center at
OSU.  We envision all our activities as
continuously evolving to accommodate new scientific
developments and to improve service. Our commitment
is long-term, and we are open to suggestions.  We
expect that both the collections and the database
will be expanding rapidly for the foreseeable
future. We intend to keep both current.

     Thank you for your interest and support.  IF
YOU HAVE RECEIVED A QUESTIONNAIRE AND HAVE NOT
COMPLETED IT, PLEASE HELP US AND THE COMMUNITY BY
DOING SO NOW!  If you have any questions, feel free
to contact us directly.

Sakti Pramanik
MSU Department of Computer Science

Randy Scholl
Arabidopsis Biological Resource Center 
     at Ohio State
1735 Neil Ave.
Columbus, OH 43210

Phone: 614-292-9371
Fax:   614-292-0603
E-mail: arabidopsis+ at osu.edu

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