Meeting on Interconnection of Molecular Biology Databases

Peter Karp pkarp at ai.sri.com
Fri Jan 21 00:08:58 EST 1994



     *****************   CALL FOR PARTICIPATION   *****************

                    Meeting on the Interconnection of 
                        Molecular Biology Databases

                          August 9-12, 1994
                         Stanford  University

     Organizer                               DEADLINES
     Peter D. Karp, SRI International        Abstracts due March 11, 1994

                        Program Committee

Robert Robbins, Johns Hopkins U       Chris Fields, TIGR
David George, NBRF                    Tim Finin, U of Maryland
George Michaels, George Mason U       Michel Noordewier, Rutgers U
Chris Overton, U of Pennsylvania      Susan Davidson, U of Pennsylvania
Dan Davison, U of Houston             Xiaolei Qian, SRI International
Robert Murphy, Carnegie-Mellon U      Richard Lathrop, MIT
Victor Markowitz, Lawrence Berkeley Laboratory


A meeting on the Interconnection of Molecular Biology Databases will
take place at Stanford University in the San Francisco Bay Area,
August 9-12, 1994.  The meeting will bring together biologists,
computer scientists, and bioinformatics researchers who are interested
in the problem of interoperation of the growing number of distributed,
heterogeneous databases and knowledge bases that serve molecular
biology and genome researchers.  

The premise behind this meeting is that the roughly 100 existing
molecular biology databases will be of much greater value to molecular
biologists when interconnected than in their current isolated states.
There is tremendous synergy between electronic data repositories in
molecular biology; once they are interconnected, scientists will be
able to integrate diverse sources of information to answer questions
that are laborious or impossible to tackle today.  Interoperation of
heterogeneous databases is a hot research topic in computer science.
This meeting is an exciting opportunity for bioinformatics workers to
learn about recent advances in computer science, and for computer
scientists to acquire a set of challenge problems in a real-world
domain.  Molecular biology databases have complex semantics, and
utilize diverse data models and platforms, thereby providing a rich
testbed for newly developed techniques for interoperation.

The subject matter of the meeting will include, but will not be
limited to, the following topics:

  o Query languages for multidatabase queries

  o Tools for schema management and schema integration

  o Approaches to interconversion among data models and data formats

  o Tradeoffs between tight and loose database integration

  o Intelligent software agents for locating information in
    the biomatrix

  o Relevant standards activities

  o Understanding the schemas of existing molecular biology databases

  o Properties of existing molecular biology databases that impose
    constraints on their interconnection

  o Research problems in biology that would benefit from database
    interconnection

  o Current computer science research projects involving interconnection
    of heterogeneous databases

  o Current research projects in interconnection of molecular biology
    databases

  o Organizational impediments and motivations for interconnection

The central goals of the meeting are to stimulate discussion, exchange
of ideas, and interdisciplinary research projects between computer
scientists who work in the area of interconnecting heterogeneous
databases, and the biologists and bioinformatics researchers who
develop and use molecular biology databases.  Computer scientists will
learn about the properties of existing databases and the requirements
that bioinformatics researchers will have for interconnection.  The
participants will identify challenge queries and computations of
interest that span multiple databases.  Bioinformatics researchers
will be exposed to technologies and research directions for
interconnection that are under development by computer science
researchers.

A second, more practical goal of the meeting is to work toward
development of a global, multi-database schema for existing
molecular biology databases, that is, to encode the schemas of a
variety of molecular biology databases in a common representation.
Creation of a global schema is one possible first step toward
interconnecting these databases, and will be a valuable exercise for
learning about and evaluating existing tools for the management of
database schemas.  Participants will attack this problem during working
sessions at the meeting.  Participants will attempt to encode the
schemas of several molecular biology databases using schema-definition
systems such as OPM (the Object-Protocol Model -- an object-oriented
system-independent data model developed at Lawrence Berkeley
Laboratory), and Ontolingua (a knowledge sharing tool under
development at Stanford University).

Participation in the meeting will be by invitation, based on abstracts
submitted by prospective participants.  Abstracts should be 2-4 pages
in length and should consist of a description of past or current
research or research interests (e.g., an overview of an approach to
database interoperation) or a position statement by the applicant
(e.g., a description of a biological problem that could be solved
given facile access to multiple databases).  Some participants will be
selected to give talks or poster presentations at the meeting, and the
submitted abstracts will be distributed as a collection at the
meeting.  Please submit abstracts electronically to the address
mimbd-abstracts at ai.sri.com; abstracts must be composed using the
template at the end of this message.

A limited amount of financial support for participant's travel and
lodging costs for has been provided by the National Science Foundation
and the Biomatrix Society.  Please indicate at the top of the
submitted abstract whether you require support.  Actual support
provided may not cover participants full costs, and will be based on
the number of requests, and the total expenses and distance traveled
by each attendee.  The MIMBD meeting will directly precede the
Conference on Intelligent Systems for Molecular Biology, which will be
held at Stanford from August 15-17, 1994.  This arrangement will allow
attendees of both meetings to combine travel expenses.  For information
on ISMB-94, send mail to ismb at nlm.nih.gov.


Peter D. Karp, Ph.D.
Artificial Intelligence Center
SRI International
333 Ravenswood Ave, EJ 229
Menlo Park, CA  94025
voice: 415-859-6375
fax: 415-859-3735
pkarp at ai.sri.com


                             Important dates:

Abstracts must be submitted by March 11, 1994.

Notification of accepted abstracts and travel awards by April 29, 1994.

Final formatted abstracts due by June 15, 1994.



                            Application Form

Please edit the for below to include the requested information, and
send the completed form by electronic mail to the address
mimbd-abstracts at ai.sri.com.  

----------------------------  cut here  ------------------------


Name: 

Institution: 

Surface mail address: 

Email address: 

Fax telephone number: 

Voice telephone number: 

Do you request travel support?   YES / NO

What type of presentation would you like to make?
TALK / POSTER / NEITHER

Include a 2-4 page abstract in the space below as simple ASCII text
with no embedded formatting commands (authors will later resubmit
accepted abstracts for inclusion in a simple workshop proceedings).



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