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Human Genome News Archive Edition

Human Genome News, April-June 1996;7(6)

GDB-LBNL Collaboration Adds Up to 6.0

The recent overhaul of the database architecture is not only a major achievement in making GDB a richer, more complete representation of the current scientific understanding of genomic information; it also represents the culmination of a successful scientific collaboration. In an intense 2-year effort, teams at Lawrence Berkeley National Laboratory (LBNL) and GDB used LBNL's Object Protocol Model (OPM) software to develop the GDB 6.0 schema and underlying Sybase databases.

OPM provides a single high-level interface to GDB's underlying genomic databases. "OPM makes the underlying database transparent, so you don't have to worry about the database management system used for implementing the database," says Victor Markowitz, leader of the LBNL group.

Markowitz and GDB's Director of Informatics Ken Fasman began discussing a collaboration in February 1994. Even though GDB staff members were impressed with OPM's potential, they were concerned that it had been used only on smaller database projects, not something as complex as GDB with its many different types of object classes. However, they had a strong incentive to reorganize the database to meet future needs.

"Initially, the research community using GDB was small, directly involved, and familiar with the early genomics research and its representation within GDB," says GDB's Bob Cottingham. "As the genome project expanded, the community of researchers interested in GDB grew rapidly and the need arose for a high-level data model and interface expressed in terms that were clearer to biological researchers."

Adding to the problems expected with implementing the OPM software were the challenges of coordinating a project across a continent. Electronic communication sped up the collaboration but stymied teamwork, making personal interactions important.

"We had regular meetings, a video conference, and many phone calls. When requirements changed, sometimes communications got scrambled. However, the commitment on both sides, as well as patience and trust, kept us going," says Markowitz.

Cooperation between the two organizations extended past the Fasman-Markowitz connection.

"Although Victor and I both worked very hard to make this collaboration a reality," says Fasman, "most important were the dedication and mutual respect in the working relationships among GDB staff members Stan Letovsky, Peter Li, and Krishna Palaniappan and OPM project members Amy Chen and Ernie Szeto."

Earlier this year at the DOE Santa Fe contractor-grantee workshop, GDB staff demonstrated the newly released Version 6.0. One of the primary advantages is its flexibility in allowing minor software changes to be made continuously and transparently. Previously, most changes had to be held for major new releases.

As expected, GDB 6.0 is requiring some user adjustments. "For GDB users, switching to the new version is like going from driving a car to piloting an F-16," Cottingham said. "It will take awhile for people to adapt to the new paradigms. Previously, our database modeling was all done directly at the relational level, which made it difficult to understand. OPM is a major improvement."

[Murray Browne, HGMIS]


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Human Genome Program, U.S. Department of Energy, Human Genome News (v7n6).

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.