Introduction to the Workshop
URLs Provided by Attendees

Abstracts

Mapping

Informatics

Sequencing

Instrumentation

Ethical, Legal, and Social Issues

Infrastructure

The electronic form of this document may be cited in the following style:
Human Genome Program, U.S. Department of Energy, DOE Human Genome Program Contractor-Grantee Workshop IV, 1994.

Abstracts scanned from text submitted for November 1994 DOE Human Genome Program Contractor-Grantee Workshop. Inaccuracies have not been corrected.

The GDB Human Genome Data Base Version 6.0

Kenneth H. Fasman, A. Jamie Cuticchia, and David T. Kingsbury
Division of Biomedical Information Sciences, Johns Hopkins University School of Medicine, 2024 E. Monument St., Baltimore MD 21205-2100

The Genome Data Base is currently undergoing a major restructuring. These changes are intended to address a number of long-standing inadequacies in the design and policies of the database. In addition, they will better prepare GDB for participation in the planned federation of biological databases.

Chief among the planned improvements are changes to the representation of mapping data in GDB. The database is being reorganized around a core of derived order and distance data from "first order" genetic and physical maps and "second order" integrated (consensus) maps of the human genome. This information will be reinforced by additional raw mapping data where appropriate. For example, while the CEPH and CHLC databases provide raw linkage data to the public, no equivalent resource exists for YAC/STS content data. GDB V6 will provide one.

The new database will be organized on a revised editorial model which differentiates between original and consensus data. GDB V6 will allow direct user submission and updates on those submissions, along with third-party annotation of those data. In addition, consensus data such as maps and nomenclature and summaries of (possibly conflicting) user data will be maintained by the HUGO editorial committees.

Version 6 of the Genome Data Base is using object-oriented data modeling and software development on both the client and server sides. An object-oriented data model is being implemented on top of a Sybase relational database using the Object Protocol Model (OPM) developed by Victor Markowitz and his colleagues at the Lawrence Berkeley Laboratory. Client software is being written using C++ and a platform-independent development library (Galaxy, Visix Software Inc.) which will allow one set of programs to access GDB data from Windows PC's, Macs, and UNIX X Windows systems.

Additional design improvements will better allow the Genome Data Base to participate in the proposed federation of genomic databases. GDB V6 will feature increased modularity of both applications and databases. The current monolithic database is being replaced by a "minifederation" of more normalized databases, including separate databases for mapping data, polymorphisms, phenotypes, genomic literature, and contact information. The current monolithic client application will be replaced by a collection of specialized modules that can interact using standard interprocess communication protocols. These modules will then be more easily incorporated into third party software systems. Some isolation of the application software from the schema and database management system will be realized through the implementation of a GDB "object broker." The object broker will provide both query and edit functionality, and can be used to work with the database in both interactive and batch modes.