The next Step: Exploring the Proteome:
Translation and Beyond

Building a foundation of protein knowledge to support post-genomic research:
The BioKnowledge Library Project

James I. Garrels, Ph.D. President, PROTEOME Division, Incyte Genomics, Inc.


Abstract:

Building a foundation of protein knowledge to support post-genomic research: The BioKnowledge Library Project The accumulated knowledge of proteins is vast and growing ever more rapidly. Proteomic studies increasingly demand rapid access to accumulated knowledge for hundreds or thousands of proteins at a time in order to properly interpret each new experiment. The research literature, which stores protein knowledge in millions of scattered articles, is no longer an adequate medium for rapid access to protein knowledge. We are using large-scale curation by expert human curators to build a new repository, the BioKnowledge Library, in which the core knowledge for each protein can be accessed from one Web page. This project relies on several levels of annotation: 1) defining the sequences of the expressed proteins, 2) defining the patterns of protein expression by cell type and tissue, 3) defining the interactions that occur between proteins, and 4) capturing the even greater complexities of ligand binding, post-translational modification, and subcellular localization that constitute much of regulation and signaling. The presentation format and underlying data structure are designed so that others can build more specialized databases and analysis packages onto the knowledge foundation in the BioKnowledge Library.

Biographical sketch:

James I. Garrels, Principal Investigator

Educational Experience
California Institute of Technology, Pasadena, CA B.S. 1971 Biology and Physics
University of California, San Diego, CA Ph.D. 1978 Biology

Professional Experience
Feb. 1995 - present President and CEO, Proteome, Inc.
1993 - Feb, 1995 Visiting Scientist, Harvard Medical School, Boston, MA,
1985 - Jan, 1995 Senior Staff Scientist and Director of the QUEST Protein Database Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
1980 - 1985 Senior Staff Investigator, Cold Spring Harbor Laboratory.
1979 - 1980 Staff Investigator, Cold Spring Harbor Laboratory.
1978 - 1979 Postdoctoral Fellow, Cold Spring Harbor Laboratory.

Awards and Memberships
Tau Beta Pi
American Society for Cell Biology
American Society for Biochemistry and Molecular Biology
Genetics Society of America
American Society for Microbiology
American Electrophoresis Society
Scientific Advisory Board, Protein Databases Inc. (1983-1988)

Outside Activities
1983-1988 Consultant, Protein Databases Inc.
1988-1994 Consultant, Millipore Corporation.

Bibliography
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J.I. Garrels, C.S. McLaughlin, J.R. Warner, B. Futcher, G.I. Latter, R. Kebayashi, B. Schwender, T. Volpe, D.S. Anderson, R. Mesquita-Fuentes, W.E. Payne. (1997) Proteome studies of Saccharomyces cerevisiae: Identification and characterization of abundant proteins. Electrophoresis.18: 1347-1360.
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J.I. Garrels (1989) The QUEST system for quantitative analysis of two-dimensional gels. J. Biol. Chem, 264: 5269-5282.
M.B. Mathews, R.M. Bernstein, B.R. Franza and J.I. Garrels (1984) Identity of the proliferating cell nuclear antigen and cyclin. Nature, 309: 374-6.
J.I. Garrels, J.T. Farrar and C.B. Burwell IV (1984) The QUEST system for computer-analyzed two-dimensional electrophoresis of proteins., In: Two-dimensional Gel Electrophoresis: Methods and Application, (ed. J.E. Celis and R. Bravo), pp. 37-91, Academic Press, New York.
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J.I. Garrels and D. Schubert (1979) Modulation of protein synthesis by nerve growth factor. J. Biol. Chem., 254: 7978-7985.
J.I. Garrels (1979) Two-dimensional gel electrophoresis and computer analysis of proteins synthesized by clonal cell lines. J. Biol. Chem., 254: 7961-7977.
T. Hunter and J.I. Garrels (1977) Characterization of the mRNAs for , ß, and actin. Cell, 12: 767-781.

Contact Information:

James I. Garrels, Ph.D., President, PROTEOME Division, Incyte Genomics, Inc., Suite 435M, 100 Cummings Center, Beverly, MA 01915, Tel: (978) 922-1643, Fax: (978) 922-3971, email: jg@proteome.com