title: EcoCyc: a comprehensive database resource for Escherichia coli.
abstract: The EcoCyc database (http://EcoCyc.org/) is a comprehensive source of information on the biology of the prototypical model organism Escherichia coli K12. The mission for EcoCyc is to contain both computable descriptions of, and detailed comments describing, all genes, proteins, pathways and molecular interactions in E.coli. Through ongoing manual curation, extensive information such as summary comments, regulatory information, literature citations and evidence types has been extracted from 8862 publications and added to Version 8.5 of the EcoCyc database. The EcoCyc database can be accessed through a World Wide Web interface, while the downloadable Pathway Tools software and data files enable computational exploration of the data and provide enhanced querying capabilities that web interfaces cannot support. For example, EcoCyc contains carefully curated information that can be used as training sets for bioinformatics prediction of entities such as promoters, operons, genetic networks, transcription factor binding sites, metabolic pathways, functionally related genes, protein complexes and protein-ligand interactions.
authors.affiliation: SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA.
authors.forename: Ingrid M
authors.initials: IM
authors.lastname: Keseler
authors.forename: Julio
authors.initials: J
authors.lastname: Collado-Vides
authors.forename: Socorro
authors.initials: S
authors.lastname: Gama-Castro
authors.forename: John
authors.initials: J
authors.lastname: Ingraham
authors.forename: Suzanne
authors.initials: S
authors.lastname: Paley
authors.forename: Ian T
authors.initials: IT
authors.lastname: Paulsen
authors.forename: Martín
authors.initials: M
authors.lastname: Peralta-Gil
authors.forename: Peter D
authors.initials: PD
authors.lastname: Karp
mesh_terms: D019295:Computational Biology; D030541:Databases, Genetic; D048168:Escherichia coli K12 / Q000235:genetics* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics* / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D023281:Genomics; D012984:Software; D014584:User-Computer Interface
chemical_list: D029968:Escherichia coli Proteins