SRI International (SRI) and The Carnegie Institution of Washington (Carnegie) propose to expand the MetaCyc database (DB) and the Pathway Tools software used to visualize, query, and edit MetaCyc. MetaCyc describes metabolic pathways in a wide variety of microorganisms and plants. The DB contains extensive information about pathways (including their reactions, substrates, comments, and literature citations) and about enzymes (including their activators, inhibitors, cofactors, subunit composition, and substrate specificity). MetaCyc is a resource for several applications. As a reference DB of pathways and enzymes, MetaCyc can be used in conjunction with SRI's PathoLogic program to predict the metabolic pathway complements of organisms from their annotated genomes. MetaCyc also serves as a readily accessible comprehensive resource on microbial and plant pathways for genome analysis, basic research and education, metabolic engineering, and systems biology. We propose to expand MetaCyc and to make it more comprehensive to increase its value to all these applications. ? ? This project involves the continued curation of new and existing pathways in MetaCyc. MetaCyc already describes most of the well-established pathways that are ubiquitous to microorganisms and to plants. The goal of this project is to add more breadth to MetaCyc by adding newly discovered pathways and pathways that are diverse among microorganisms, and plants, such as secondary metabolism. As part of this project, SRI also proposes to further develop the Pathways Tools software by enhancing (1) visual displays and internal representations of pathways and chemical compounds, (2) user querying capabilities, and (3) software editing capabilities. ? ?

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Exploratory/Developmental Grants Phase II (R33)
Project #
5R33GM070065-03
Application #
7020676
Study Section
Special Emphasis Panel (ZRG1-SSS-H (90))
Program Officer
Jones, Warren
Project Start
2004-03-01
Project End
2008-02-28
Budget Start
2006-03-01
Budget End
2008-02-28
Support Year
3
Fiscal Year
2006
Total Cost
$1,121,979
Indirect Cost
Name
Sri International
Department
Type
DUNS #
009232752
City
Menlo Park
State
CA
Country
United States
Zip Code
94025
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Paley, Suzanne M; Karp, Peter D (2006) The Pathway Tools cellular overview diagram and Omics Viewer. Nucleic Acids Res 34:3771-8
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Green, M L; Karp, P D (2005) Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers. Nucleic Acids Res 33:4035-9
Karp, Peter D (2004) Call for an enzyme genomics initiative. Genome Biol 5:401