title: YMDB: the Yeast Metabolome Database.
abstract: The Yeast Metabolome Database (YMDB, http://www.ymdb.ca) is a richly annotated 'metabolomic' database containing detailed information about the metabolome of Saccharomyces cerevisiae. Modeled closely after the Human Metabolome Database, the YMDB contains >2000 metabolites with links to 995 different genes/proteins, including enzymes and transporters. The information in YMDB has been gathered from hundreds of books, journal articles and electronic databases. In addition to its comprehensive literature-derived data, the YMDB also contains an extensive collection of experimental intracellular and extracellular metabolite concentration data compiled from detailed Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) metabolomic analyses performed in our lab. This is further supplemented with thousands of NMR and MS spectra collected on pure, reference yeast metabolites. Each metabolite entry in the YMDB contains an average of 80 separate data fields including comprehensive compound description, names and synonyms, structural information, physico-chemical data, reference NMR and MS spectra, intracellular/extracellular concentrations, growth conditions and substrates, pathway information, enzyme data, gene/protein sequence data, as well as numerous hyperlinks to images, references and other public databases. 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 S. cervesiae'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 yeast biologists, systems biologists, the industrial fermentation industry, as well as the beer, wine and spirit industry.
authors: Department of Computing Science, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E8, Canada.
authors: Timothy
authors: T
authors: Jewison
authors: Craig
authors: C
authors: Knox
authors: Vanessa
authors: V
authors: Neveu
authors: Yannick
authors: Y
authors: Djoumbou
authors: An Chi
authors: AC
authors: Guo
authors: Jacqueline
authors: J
authors: Lee
authors: Philip
authors: P
authors: Liu
authors: Rupasri
authors: R
authors: Mandal
authors: Ram
authors: R
authors: Krishnamurthy
authors: Igor
authors: I
authors: Sinelnikov
authors: Michael
authors: M
authors: Wilson
authors: David S
authors: DS
authors: Wishart
mesh_terms: D016208:Databases, Factual; D005800:Genes, Fungal; D020407:Internet; D013058:Mass Spectrometry; D055442:Metabolome; D055432:Metabolomics; D019906:Nuclear Magnetic Resonance, Biomolecular; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism
chemical_list: D029701:Saccharomyces cerevisiae Proteins