The Genome Data Base V6*

Kenneth H. Fasman, Stanley I. Letovsky, Peter Li, Robert W. Cottingham, and David T. Kingsbury

Division of Biomedical Information Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2236

GDB has been completely redesigned to address some well-recognized shortcomings, such as:

• Text-based display of map information.
• Difficulties casual users have in finding information of common interest, such as gene descriptions.
• Data acquisition and curation being funneled through HUGO committees and GDB staff.

The focus of the development of GDB 6.0 was the redesign of the database schema and front-end interfaces to address these inadequacies, including:

• An improved data representation of genetic and physical maps allowing for graphical map visualization and querying, including display of multiple aligned maps.
• A new curatorial model allowing direct community editing and curation, including third-party annotation to support a greater diversity of opinion about features of the genome and their location.
• An improved model for gene information including links to databases describing function, structure, products, expression, and associated phenotypes.

The development of GDB 6.0 utilizes several new technologies including an object-oriented data model, object broker, data-driven WWW interface, and graphical interfaces for most popular computer platforms.

With 6.0, GDB staff hope to increasingly promote community participation in the design process regarding both the data model and front-end interfaces, so that we can provide the tools necessary to support the Human Genome Project.

Future enhancements to GDB will include improved map editing, an integrated editing environment, querying and browsing, integration with the GSDB Sequence Annotator and the Mouse Genome Database interfaces, and improved polymorphism and mutation representation.

*Supported by the U.S. Department of Energy (DE-FC02-9ER6130), the U.S. National Institutes of Health. and the Science and Technology Agency of Japan, with additional support from the Medical Research Council of the United Kingdom, the INSERM of France, and the European Union.