Karp, P.D. and Paley, S.M.. "Integrated access to metabolic and genomic data." J Comput Biol. 3
(1).
1996.
pp. 191-212.
[ .pdf ] [ .ps ] [ PubMed ]
The EcoCyc system consists of a knowledge base (KB) that describes the genes and intermediary metabolism of Escherichia coli, and a graphical user interface (GUI) for accessing that knowledge. This paper addresses two problems: How can we create a GUI that provides integrated access to metabolic and genomic data? We describe the design and implementation of visual presentations that closely mimic those found in the biology literature, and that offer hypertext navigation among related entities, and multiple views of the same entity. We employ a frame knowledge representation system (FRS) called HyperTHEO to manage the EcoCyc knowledge base. Among the advantages of FRSs are an expressive data model for capturing the complexities of biological information, and schema-evolution capabilities that facilitate the constant schema changes that biological databases tend to undergo. HyperTHEO also includes rule-based inference facilities that are the foundation of expert systems, a constraint language for maintaining data integrity, and a declarative query language. A graphic KB editor and browser allow the EcoCyc developers to interactively inspect and modify this evolving KB.
Keywords: *Artificial Intelligence ; Computer Communication Networks ; Computer Graphics ; Computers ; *Database Management Systems ; Escherichia coli_*genetics ; Escherichia coli_*metabolism ; *Genome ; Bacterial ; Programming Languages ; Systems Integration ; User-Computer Interface
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., 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