Meeting on the Interconnection of Molecular Biology Databases

Reinhard Doelz doelz
Fri Sep 30 01:55:24 EST 1994

[ Article crossposted from bionet.molbio.genome-program ]
[ Author was Peter Karp ]
[ Posted on 29 Sep 1994 15:16:24 -0700 ]

There is tremendous synergy between the roughly 100 existing
molecular-biology databases.  Once these databases are interconnected,
biologists will be able to integrate diverse sources of information to
answer questions that are laborious or impossible to tackle today.

A workshop entitled ``Interconnection of Molecular Biology Databases''
was held at Stanford University on August 9-12, 1994.  The workshop
was sponsored by the National Science Foundation and by the Biomatrix
Society, and was organized by Dr. Peter D. Karp of the SRI
International Artificial Intelligence Center, with program committee
assistance.  The meeting brought together 55 bioinformatics
researchers, computer scientists, and biologists from nine countries.
The participants included members of genome centers at Baylor College
of Medicine, the University of Pennsylvania, the Whitehead Institute,
Lawrence Berkeley Laboratory, Lawrence Livermore National Laboratory,
Genethon, and the Sanger Centre.

The workshop surveyed existing molecular-biology databases and the
requirements for interoperation among them.  Computer scientists
presented an overview of the database-operation problem, and of
techniques for solving it.  Participants described a wide range of
approaches to interoperation of molecular-biology databases, that are
generating practical results.  Existing systems allow multidatabase
queries to databases such as Genbank, GDB, and PDB.  There now exists
no single, final resolution to the interoperation problem.  Current
approaches differ along a variety of dimensions including ability to
handle complex queries, difficulty of implementation, required user
expertise, and scalability.  An understanding of these dimensions is
important when deciding what techniques to employ for a given
collection of databases and a given scientific community.  The
workshop identified a number of barriers to interoperation, such as
resistance to standards, inaccessibility of existing databases to
structured query via Internet, and poor documentation of many
databases.  But interoperation is proceeding at a rapid pace that
promises to fuel scientific discovery.

Scientists can use the Internet to access the following hypertext
documents from the SRI International Web servers starting at URL

o The final report of the workshop

o Abstracts from the workshop participants

o The meeting agenda

o The call for participation and summary of workshop goals

o Contact information for workshop participants 

o A summary of biological databases, including Web pointers to
  many of them
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