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NOTICE: The project that is the subject of this report was approved by the Governing Board of the National Research Council, whose members are drawn from the councils of the National Academy of Sciences, the National Academy of Engineering, and the Institute of Medicine. The members of the committee responsible for the report were chosen for their special competences and with regard for appropriate balance.
This report has been prepared with funds provided by the Department of Energy, grant DEFG02-94ER61939, and the National Cancer Institute, contract N01-OD-4-2139.
ISBN 0-309-07256-5
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THE NATIONAL ACADEMIES
National Academy of Sciences
National Academy of Engineering
Institute of Medicine
National Research Council
The National Academy of Sciences is a private, nonprofit, self-perpetuating society of distinguished scholars engaged in scientific and engineering research, dedicated to the furtherance of science and technology and to their use for the general welfare. Upon the authority of the charter granted to it by the Congress in 1863, the Academy has a mandate that requires it to advise the federal government on scientific and technical matters. Dr. Bruce M. Alberts is president of the National Academy of Sciences.
The National Academy of Engineering was established in 1964, under the charter of the National Academy of Sciences, as a parallel organization of outstanding engineers. It is autonomous in its administration and in the selection of its members, sharing with the National Academy of Sciences the responsibility for advising the federal government. The National Academy of Engineering also sponsors engineering programs aimed at meeting national needs, encourages education and research, and recognizes the superior achievements of engineers. Dr. William A. Wulf is president of the National Academy of Engineering.
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The National Research Council was organized by the National Academy of Sciences in 1916 to associate the broad community of science and technology with the Academy's purposes of furthering knowledge and advising the federal government. Functioning in accordance with general policies determined by the Academy, the Council has become the principal operating agency of both the National Academy of Sciences and the National Academy of Engineering in providing services to the government, the public, and the scientific and engineering communities. The Council is administered jointly by both Academies and the Institute of Medicine. Dr. Bruce M. Alberts and Dr. William A. Wulf are chairman and vice chairman, respectively, of the National Research Council.
PLANNING GROUP FOR THE WORKSHOP ON BIOINFORMATICS: CONVERTING DATA TO KNOWLEDGE
DAVID EISENBERG,
University of California, Los Angeles, California
DAVID J. GALAS,
Keck Graduate Institute of Applied Life Sciences, Claremont, California
RAYMOND L. WHITE,
University of Utah, Salt Lake City, Utah
Science Writer
ROBERT POOL,
Tallahassee, Florida
Staff
JOAN ESNAYRA, Study Director
JENNIFER KUZMA, Program Officer
NORMAN GROSSBLATT, Editor
DEREK SWEATT, Project Assistant
Acknowledgments
The steering committee acknowledges the valuable contributions to this workshop of Susan Davidson, University of Pennsylvania; Richard Karp, University of California, Berkeley; and Perry Miller, Yale University. In addition, the steering committee thanks Marjory Blumenthal and Jon Eisenberg, of the NRC Computer Science and Telecommunications Board, for helpful input.
BOARD ON BIOLOGY
MICHAEL T. CLEGG, Chair,
University of California, Riverside, California
JOANNA BURGER,
Rutgers University, Piscataway, New Jersey
DAVID EISENBERG,
University of California, Los Angeles, California
DAVID J. GALAS,
Darwin Technologies, Seattle, Washington
DAVID V. GOEDDEL,
Tularik, Inc., San Francisco, California
ARTURO GOMEZ-POMPA,
University of California, Riverside, California
COREY S. GOODMAN,
University of California, Berkeley, California
CYNTHIA J. KENYON,
University of California, San Francisco, California
BRUCE R. LEVIN,
Emory University, Atlanta, Georgia
ELLIOT M. MEYEROWITZ,
California Institute of Technology, Pasadena, California
ROBERT T. PAINE,
University of Washington, Seattle, Washington
RONALD R. SEDEROFF,
North Carolina State University, Raleigh, North Carolina
ROBERT R. SOKAL,
State University of New York, Stony Brook, New York
SHIRLEY M. TILGHMAN,
Princeton University, Princeton, New Jersey
RAYMOND L. WHITE,
University of Utah, Salt Lake City, Utah
Staff
RALPH DELL, Acting Director (until August 2000)
WARREN MUIR, Acting Director (as of August 2000)
COMMISSION ON LIFE SCIENCES
MICHAEL T. CLEGG, Chair,
University of California, Riverside, California
FREDERICK R. ANDERSON,
Cadwalader, Wickersham and Taft, Washington, D.C.
PAUL BERG,
Stanford University, Stanford, California
JOANNA BURGER,
Rutgers University, Piscataway, New Jersey
JAMES CLEAVER,
University of California, San Francisco, California
DAVID EISENBERG,
University of California, Los Angeles, California
NEAL L. FIRST,
University of Wisconsin, Madison, Wisconsin
DAVID J. GALAS,
Keck Graduate Institute of Applied Sciences, Claremont, California
DAVID V. GOEDDEL,
Tularik, Inc., San Francisco, California
ARTURO GOMEZ-POMPA,
University of California, Riverside, California
COREY S. GOODMAN,
University of California, Berkeley, California
JON W. GORDON,
Mount Sinai School of Medicine, New York, New York
DAVID G. HOEL,
Medical University of South Carolina, Charleston, South Carolina
BARBARA S. HULKA,
University of North Carolina, Chapel Hill, North Carolina
CYNTHIA J. KENYON,
University of California, San Francisco, California
BRUCE R. LEVIN,
Emory University, Atlanta, Georgia
DAVID M. LIVINGSTON,
Dana-Farber Cancer Institute, Boston, Massachusetts
DONALD R. MATTISON,
March of Dimes, White Plains, New York
ELLIOT M. MEYEROWITZ,
California Institute of Technology, Pasadena, California
ROBERT T. PAINE,
University of Washington, Seattle, Washington
RONALD R. SEDEROFF,
North Carolina State University, Raleigh, North Carolina
ROBERT R. SOKAL,
State University of New York, Stony Brook, New York
CHARLES F. STEVENS,
The Salk Institute for Biological Studies, La Jolla, California
SHIRLEY M. TILGHMAN,
Princeton University, Princeton, New Jersey
RAYMOND L. WHITE,
University of Utah, Salt Lake City, Utah
Staff
WARREN MUIR, Executive Director
Preface
In 1993 the National Research Council's Board on Biology established a series of forums on biotechnology. The purpose of the discussions is to foster open communication among scientists, administrators, policy-makers, and others engaged in biotechnology research, development, and commercialization. The neutral setting offered by the National Research Council is intended to promote mutual understanding among government, industry, and academe and to help develop imaginative approaches to problem-solving. The objective, however, is to illuminate issues, not to resolve them. Unlike study committees of the National Research Council, forums cannot provide advice or recommendations to any government agency or other organization. Similarly, summaries of forums do not reach conclusions or present recommendations, but instead reflect the variety of opinions expressed by the participants. The comments in this report reflect the views of the forum's participants as indicated in the text.
For the first forum, held on November 5, 1996, the Board on Biology collaborated with the Board on Agriculture to focus on intellectual property rights issues surrounding plant biotechnology. The second forum, held on April 26, 1997, and also conducted in collaboration with the Board on Agriculture, was focused on issues in and obstacles to a broad genome project with numerous plant and animal species as its subjects. The third forum, held on November 1, 1997, focused on privacy issues and the desire to protect people from unwanted intrusion into their medical records. Proposed laws contain broad language that could affect bio-
medical and clinical research, in addition to the use of genetic testing in research.
After discussions with the National Cancer Institute and the Department of Energy, the Board on Biology agreed to run a workshop under the auspices of its forum on biotechnology titled “Bioinformatics: Converting Data to Knowledge” on February 16, 2000. A workshop planning group was assembled, whose role was limited to identifying agenda topics, appropriate speakers, and other participants for the workshop. Topics covered were: database integrity, curation, interoperability, and novel analytic approaches. At the workshop, scientists from industry, academe, and federal agencies shared their experiences in the creation, curation, and maintenance of biologic databases. Participation by representatives of the National Institutes of Health, National Science Foundation, US Department of Energy, US Department of Agriculture, and the Environmental Protection Agency suggests that this issue is important to many federal bodies. This document is a summary of the workshop and represents a factual recounting of what occurred at the event. The authors of this summary are Robert Pool and Joan Esnayra, neither of whom were members of the planning group.
This workshop summary has been reviewed in draft form for accuracy by individuals who attended the workshop and others chosen for their diverse perspectives and technical expertise in accordance with procedures approved by the NRC's Report Review Committee. The purpose of this independent review is to assist the NRC in making the published document as sound as possible and to ensure that it meets institutional standards. We wish to thank the following individuals, who are neither officials nor employees of the NRC, for their participation in the review of this workshop summary:
Warren Gish, Washington University School of Medicine
Anita Grazer, Fairfax County Economic Development Authority
Jochen Kumm, University of Washington Genome Center
Chris Stoeckert, Center for Bioinformatics, University of Pennsylvania
While the individuals listed above have provided many constructive comments and suggestions, it must be emphasized that responsibility for the final content of this document rests entirely with the authors and the NRC.
Joan Esnayra
Study Director