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. ? ?
| Caspi, Ron; Foerster, Hartmut; Fulcher, Carol A et al. (2008) The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res 36:D623-31 |
| Caspi, Ron; Karp, Peter D (2007) Using the MetaCyc pathway database and the BioCyc database collection. Curr Protoc Bioinformatics Chapter 1:Unit1.17 |
| Paley, Suzanne M; Karp, Peter D (2006) The Pathway Tools cellular overview diagram and Omics Viewer. Nucleic Acids Res 34:3771-8 |
| Green, M L; Karp, P D (2006) The outcomes of pathway database computations depend on pathway ontology. Nucleic Acids Res 34:3687-97 |
| Krummenacker, Markus; Paley, Suzanne; Mueller, Lukas et al. (2005) Querying and computing with BioCyc databases. Bioinformatics 21:3454-5 |
| Karp, Peter D; Ouzounis, Christos A; Moore-Kochlacs, Caroline et al. (2005) Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res 33:6083-9 |
| 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 |
