Karp, P.D., Riley, M., Paley, S.M., and Pellegrini-Toole, A.. "The MetaCyc Database." Nucleic Acids Res. 30
(1).
2002.
pp. 59-61.
[ .pdf ] [ PubMed ]
MetaCyc is a metabolic-pathway database that describes 445 pathways and 1115 enzymes occurring in 158 organisms. MetaCyc is a review-level database in that a given entry in MetaCyc often integrates information from multiple literature sources. The pathways in MetaCyc were determined experimentally and are labeled with the species in which they are known to occur based on literature references examined to date. MetaCyc contains extensive commentary and literature citations. Applications of MetaCyc include pathway analysis of genomes, metabolic engineering and biochemistry education. MetaCyc is queried using the Pathway Tools graphical user interface, which provides a wide variety of query operations and visualization tools. MetaCyc is available via the World Wide Web at http://ecocyc.org/ecocyc/metacyc.html, and is available for local installation as a binary program for the PC and the Sun workstation, and as a set of flatfiles. Contact metacyc-info
Keywords: Comparative Study ; Database Management Systems ; *Databases Protein ; Enzymes_chemistry ; Enzymes_*metabolism ; Genome ; Human ; Information Storage and Retrieval ; Internet ; *Metabolism
Karp, P.D., Riley, M., Paley, S.M., and Pellegrini-Toole, A.. "EcoCyc: an encyclopedia of Escherichia coli genes and metabolism." Nucleic Acids Res. 24
(1).
1996.
pp. 32-9.
[ .pdf ] [ PubMed ]
The encyclopedia of Escherichia coli genes and metabolism (EcoCyc) is a database that combines information about the genome and the intermediary metabolism of E.coli. It describes 2034 genes, 306 enzymes encoded by these genes, 580 metabolic reactions that occur in E.coli and the organization of these reactions into 100 metabolic pathways. The EcoCyc graphical user interface allows query and exploration of the EcoCyc database using visualization tools such as genomic map browsers and automatic layouts of metabolic pathways. EcoCyc spans the space from sequence to function to allow investigation of an unusually broad range of questions. EcoCyc can be thought of as both an electronic review article, because of its copious references to the primary literature, and as an in silico model of E.coli that can be probed and analyzed through computational means.
Keywords: Computer Communication Networks ; *Databases Factual ; Enzymes_metabolism ; Escherichia coli_enzymology ; Escherichia coli_*genetics ; Escherichia coli_*metabolism ; *Genome ; Bacterial ; Information Storage and Retrieval ; Software ; User-Computer Interface
Karp, P.D., Riley, M., Paley, S.M., Pellegrini-Toole, A., and Krummenacker, M.. "EcoCyc: Enyclopedia of Escherichia coli Genes and Metabolism." Nucleic Acids Res. 25
(1).
1997.
pp. 43-51.
[ .pdf ] [ PubMed ]
The Encyclopedia of Genes and Metabolism (EcoCyc) is a database that combines information about the genome and the intermediary metabolism of Escherichia coli. It describes 2970 genes of E.coli, 547 enzymes encoded by these genes, 702 metabolic reactions that occur in E.coli and the organization of these reactions into 107 metabolic pathways. The EcoCyc graphical user interface allows scientists to query and explore the EcoCyc database using visualization tools such as genomic-map browsers and automatic layouts of metabolic pathways. EcoCyc spans the space from sequence to function to allow scientists to investigate an unusually broad range of questions. EcoCyc can be thought of as both an electronic review article because of its copious references to the primary literature, and as an in silicio model of E.coli metabolism that can be probed and analyzed through computational means.
Keywords: Amino Acid Sequence ; Base Sequence ; *Databases Factual ; Escherichia coli_*genetics ; Escherichia coli_*metabolism ; *Genes Bacterial ; User-Computer Interface
Karp, P.D., Riley, M., Paley, S.M., Pellegrini-Toole, A., and Krummenacker, M.. "EcoCyc: Encyclopedia of Escherichia coli genes and metabolism." Nucleic Acids Res. 26
(1).
1998.
pp. 50-3.
[ .pdf ] [ PubMed ]
The encyclopedia of Escherichia coli genes and metabolism (EcoCyc) is a database that combines information about the genome and the intermediary metabolism of E.coli. The database describes 3030 genes of E.coli , 695 enzymes encoded by a subset of these genes, 595 metabolic reactions that occur in E.coli, and the organization of these reactions into 123 metabolic pathways. The EcoCyc graphical user interface allows scientists to query and explore the EcoCyc database using visualization tools such as genomic-map browsers and automatic layouts of metabolic pathways. EcoCyc can be thought of as an electronic review article because of its copious references to the primary literature, and as a (qualitative) computational model of E.coli metabolism. EcoCyc is available at URL http://ecocyc.PangeaSystems.com/ecocyc/
Keywords: Computer Graphics ; *Databases Factual_trends ; Encyclopedias ; Escherichia coli_*genetics ; Escherichia coli_*metabolism ; *Genes Bacterial ; User-Computer Interface
Karp, P.D., Riley, M., Paley, S.M., Pellegrini-Toole, A., and Krummenacker, M.. "Eco Cyc: encyclopedia of Escherichia coli genes and metabolism." Nucleic Acids Res. 27
(1).
1999.
pp. 55-8.
[ .pdf ] [ PubMed ]
The EcoCyc database describes the genome and gene products of Escherichia coli, its metabolic and signal-transduction pathways, and its tRNAs. The database describes 4391 genes of E.coli, 695 enzymes encoded by a subset of these genes, 904 metabolic reactions that occur in E.coli, and the organization of these reactions into 129 metabolic pathways. The EcoCyc graphical user interface allows scientists to query and explore the EcoCyc database using visualization tools such as genomic-map browsers and automatic layouts of metabolic pathways. EcoCyc has many references to the primary literature, and is a (qualitative) computational model of E. coli metabolism. EcoCyc is available at URL http://ecocyc. PangeaSystems.com/ecocyc/
Keywords: Classification ; *Databases Factual ; Enzymes_genetics ; Enzymes_metabolism ; Escherichia coli_*genetics ; Escherichia coli_*metabolism ; *Genes Bacterial ; Genome Bacterial ; Information Storage and Retrieval ; Internet ; Signal Transduction ; User-Computer Interface
Karp, P.D., Riley, M., Saier, M., Paulsen, I.T., Paley, S.M., and Pellegrini-Toole, A.. "The EcoCyc and MetaCyc databases." Nucleic Acids Res. 28
(1).
2000.
pp. 56-9.
[ .pdf ] [ PubMed ]
EcoCyc is an organism-specific Pathway/Genome Database that describes the metabolic and signal-transduction pathways of Escherichia coli, its enzymes, and-a new addition-its transport proteins. MetaCyc is a new metabolic-pathway database that describes pathways and enzymes of many different organisms, with a microbial focus. Both databases are queried using the Pathway Tools graphical user interface, which provides a wide variety of query operations and visualization tools. EcoCyc and MetaCyc are available at http://ecocyc.PangeaSystems.com/ecocyc/
Keywords: Database Management Systems ; *Databases Factual ; Escherichia coli_genetics ; Genome ; Bacterial
Karp, P.D., Riley, M., Saier, M., Paulsen, I.T., Collado-Vides, J., Paley, S.M., Pellegrini-Toole, A., Bonavides, C., and Gama-Castro, S.. "The EcoCyc Database." Nucleic Acids Res. 30
(1).
2002.
pp. 56-8.
[ .pdf ] [ PubMed ]
EcoCyc is an organism-specific pathway/genome database that describes the metabolic and signal-transduction pathways of Escherichia coli, its enzymes, its transport proteins and its mechanisms of transcriptional control of gene expression. EcoCyc is queried using the Pathway Tools graphical user interface, which provides a wide variety of query operations and visualization tools. EcoCyc is available at http://ecocyc.org/.
Keywords: Database Management Systems ; *Databases Genetic ; Escherichia coli_*genetics ; Escherichia coli_*metabolism ; Escherichia coli Proteins_*genetics ; Escherichia coli Proteins_*physiology ; Gene Expression Regulation Bacterial ; *Genome Bacterial ; Information Storage and Retrieval ; Internet ; Protein Transport ; Signal Transduction