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Human Genome News Archive Edition

Human Genome News, May 1992; 4(1)

GDB Database Access Toolkit Available

The Genome Data Base (GDB) product development staff have developed the GDB Database Access Toolkit (DAT) to aid in making genetic and physical mapping data readily available in various formats through a variety of mechanisms. The GDB DAT-an application programming interface (API) to GDB-is a collection (stored in SYBASE*) of procedures, views, triggers, rules, defaults, and C routines that reside within the database. This collection of software provides the means to access and update the database.

The NIH-DOE Ad Hoc Committee on Future Human Genome Map Databases recommended development of a stable, documented API to the database at its meeting on December 17, 1990. The GDB DAT was developed using established software-engineering practices and coding standards to create software that is well-documented, tested, and maintainable. Because DAT allows access to data independent of the physical database design, changes in the physical database schema should necessitate minimal change to front-end applications.

DAT is an important software tool for accessing data, embedding GDB functionality within other applications, and developing new tools to browse the GDB database. The toolkit will become a significant architectural component of all future GDB software products beginning with the next major release of the GDB application (version 5.0) expected this fall. Through the use of high-level stored procedures the end user will be able to retrieve data without needing to understand the physical design of the database. For example, the user might call a DAT routine by entering the GDB source identification number and receive the complete information about that reference.

As a part of GDB software architecture, DAT provides important routines that maintain both the semantic and syntactic integrity of the database by validating the data that are passed to the routines and allowing updates only upon successful validation. To ensure data integrity, DAT handles its own transaction processing, error detection, reporting, and recovery. Separation of the front-end application from database processing will facilitate migration of the GDB application to new releases of SYBASE or other vendor software and development of new applications such as graphical user interfaces. The DAT library makes existing GDB functions extensible to other applications.

*SYBASE is a trademark of Sybase, Inc.

Reported by Christopher Brunn and Francois Schiettecatte, GDB, Johns Hopkins University

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Human Genome Program, U.S. Department of Energy, Human Genome News (v4n1).

Human Genome Project 1990–2003

The Human Genome Project (HGP) was an international 13-year effort, 1990 to 2003. Primary goals were to discover the complete set of human genes and make them accessible for further biological study, and determine the complete sequence of DNA bases in the human genome. See Timeline for more HGP history.

Human Genome News

Published from 1989 until 2002, this newsletter facilitated HGP communication, helped prevent duplication of research effort, and informed persons interested in genome research.