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Suggested Citation:"Front Matter." National Research Council. 2000. Bioinformatics: Converting Data to Knowledge: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/9990.
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Bioinformatics

Converting Data to Knowledge

A Workshop Summary by

Robert Pool, Ph.D.

and

Joan Esnayra, Ph.D.

Board on Biology

Commission on Life Sciences

National Research Council

NATIONAL ACADEMY PRESS
Washington, D.C.

Suggested Citation:"Front Matter." National Research Council. 2000. Bioinformatics: Converting Data to Knowledge: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/9990.
×

NATIONAL ACADEMY PRESS
2101 Constitution Avenue Washington, D.C. 20418

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

Additional copies are available from the

National Academy Press,
2101 Constitution Ave., NW, Box 285, Washington, DC 20055; 800-624-6242 or 202-334-3313 in the Washington metropolitan area; Internet <http://www.nap.edu>.

Copyright 2000 by the National Academy of Sciences. All rights reserved.

Printed in the United States of America.

Suggested Citation:"Front Matter." National Research Council. 2000. Bioinformatics: Converting Data to Knowledge: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/9990.
×

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.

The Institute of Medicine was established in 1970 by the National Academy of Sciences to secure the services of eminent members of appropriate professions in the examination of policy matters pertaining to the health of the public. The Institute acts under the responsibility given to the National Academy of Sciences by its congressional charter to be an adviser to the federal government and, upon its own initiative, to identify issues of medical care, research, and education. Dr. Kenneth I. Shine is president of the Institute of Medicine.

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.

Suggested Citation:"Front Matter." National Research Council. 2000. Bioinformatics: Converting Data to Knowledge: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/9990.
×

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.

Suggested Citation:"Front Matter." National Research Council. 2000. Bioinformatics: Converting Data to Knowledge: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/9990.
×

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)

Suggested Citation:"Front Matter." National Research Council. 2000. Bioinformatics: Converting Data to Knowledge: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/9990.
×

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

Suggested Citation:"Front Matter." National Research Council. 2000. Bioinformatics: Converting Data to Knowledge: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/9990.
×

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-

Page viii Cite
Suggested Citation:"Front Matter." National Research Council. 2000. Bioinformatics: Converting Data to Knowledge: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/9990.
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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

Suggested Citation:"Front Matter." National Research Council. 2000. Bioinformatics: Converting Data to Knowledge: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/9990.
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Suggested Citation:"Front Matter." National Research Council. 2000. Bioinformatics: Converting Data to Knowledge: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/9990.
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 CONVERTING DATA TO KNOWLEDGE

 

23

   

 Data Mining,

 

23

   

 International Consortium for Brain Mapping,

 

25

   

 SUMMARY

 

29

   

 Appendixes

 
   

A Agenda

 

31

   

B Participant Biographies

 

33

Suggested Citation:"Front Matter." National Research Council. 2000. Bioinformatics: Converting Data to Knowledge: Workshop Summary. Washington, DC: The National Academies Press. doi: 10.17226/9990.
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Dedication

This report is dedicated to the memory of Dr. G. Christian Overton for his vision and pioneering contributions to genomic research.

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The goal of this workshop was to bring together bioinformatics stake holders from government, academe, and industry for a day of presentations and dialogue. Fifteen experts identified and discussed some of the most important issues raised by the current flood of biologic data. Topics explored included the importance of database curation, database integration and interoperability, consistency and standards in terminology, error prevention and correction, data provenance, ontology, the importance of maintaining privacy, data mining, and the need for more computer scientists with specialty training in bioinformatics. Although formal conclusions and recommendations will not come from this particular workshop, many insights may be gleaned about the future of this field, from the context of the discussions and presentations described here.

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