title: ECMDB: the E. coli Metabolome Database.
abstract: The Escherichia coli Metabolome Database (ECMDB, http://www.ecmdb.ca) is a comprehensively annotated metabolomic database containing detailed information about the metabolome of E. coli (K-12). Modelled closely on the Human and Yeast Metabolome Databases, the ECMDB contains >2600 metabolites with links to ∼1500 different genes and proteins, including enzymes and transporters. The information in the ECMDB has been collected from dozens of textbooks, journal articles and electronic databases. Each metabolite entry in the ECMDB contains an average of 75 separate data fields, including comprehensive compound descriptions, names and synonyms, chemical taxonomy, compound structural and physicochemical data, bacterial growth conditions and substrates, reactions, pathway information, enzyme data, gene/protein sequence data and numerous hyperlinks to images, references and other public databases. The ECMDB also includes an extensive collection of intracellular metabolite concentration data compiled from our own work as well as other published metabolomic studies. This information is further supplemented with thousands of fully assigned reference nuclear magnetic resonance and mass spectrometry spectra obtained from pure E. coli metabolites that we (and others) have collected. Extensive searching, relational querying and data browsing tools are also provided that support text, chemical structure, spectral, molecular weight and gene/protein sequence queries. Because of E. coli's importance as a model organism for biologists and as a biofactory for industry, we believe this kind of database could have considerable appeal not only to metabolomics researchers but also to molecular biologists, systems biologists and individuals in the biotechnology industry.
authors.affiliation: Department of Computing Science, University of Alberta, Edmonton, Alberta T6G 2E8, Canada.
authors.forename: An Chi
authors.initials: AC
authors.lastname: Guo
authors.forename: Timothy
authors.initials: T
authors.lastname: Jewison
authors.forename: Michael
authors.initials: M
authors.lastname: Wilson
authors.forename: Yifeng
authors.initials: Y
authors.lastname: Liu
authors.forename: Craig
authors.initials: C
authors.lastname: Knox
authors.forename: Yannick
authors.initials: Y
authors.lastname: Djoumbou
authors.forename: Patrick
authors.initials: P
authors.lastname: Lo
authors.forename: Rupasri
authors.initials: R
authors.lastname: Mandal
authors.forename: Ram
authors.initials: R
authors.lastname: Krishnamurthy
authors.forename: David S
authors.initials: DS
authors.lastname: Wishart
mesh_terms: D030541:Databases, Genetic; D048168:Escherichia coli K12 / Q000201:enzymology / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000378:metabolism; D020407:Internet; D055442:Metabolome / Q000235:genetics
chemical_list: D029968:Escherichia coli Proteins