Plant Genome I Conference
Town & Country Conference Center, San Diego, CA, November, 1992.
PG-I: 74pg1
COLLABORATIVE GENOME DATABASE DEVELOPMENT
John McCarthy, Genome Computing Group, 5OB-3238
Lawrence Berkeley Laboratory, Berkeley CA 94720
Lawrence Berkeley Laboratory's Genome Computing Group
provides systems integration and development for data collection,
laboratory automation,and databases. It has helped develop
species-specific databases for collaborative genome research on
soybeans, triticiae (wheat, barley, etc.), forest trees,
fruitflies, dogs, and humans. These collaborative projects help
get data from laboratory notebooks and other sources into shared
public archives such as the National Agricultural Library's Plant
Genome Database. They also serve as prototypes for new
approaches to database design, user interfaces, and data
acquisition procedures. These projects share many common needs,
and they have been working together with other such efforts to
acquire, develop, and integrate various software tools for genome
research. Two sets of software that have had the greatest impact
to date on these projects are LBL's data management tools and
ACeDB, a data management system originally developed by Richard
Durbin and Jean Thierry-Mieg for the C. elegans community. LBL's
database tools permit users to define databases graphically and
automatically generate requisite system definitions, procedures,
etc. for any of several database systems. ACEDB has become a
popular vehicle for collaborative genome databases because of its
graphical user interface, flexible data model, intuitive input
and output procedures, low installation and maintenance costs,
and ease of use. It is currently being used by over thirty
installations outside the C. elegans community. The European
Integrated Genome Database Project has successfully used LBL's
data management tools to pair ACEDB "front ends" with an
underlying relational database to integrate major genome archives
such as GDB, GenBank, and PIR. It may be a model for future
development of the U.S. Department of Agriculture's Plant Genome
Database.
Return to Previous Page or Intl-PAG Homepage