YMDB: the yeast metabolome database

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DOIResolve DOI: http://doi.org/10.1093/nar/gkr916
AuthorSearch for: ; Search for: ; Search for: ; Search for: ; Search for: ; Search for: ; Search for: ; Search for: ; Search for: ; Search for: ; Search for: ; Search for:
Journal titleNucleic Acids Research
Subjectfungal enzyme; fungal protein; amino acid sequence; enzyme analysis; fungal gene; fungal metabolism; fungal structures; fungus growth; fungus identification; gene sequence; genetic association; mass spectrometry; metabolite; metabolome; metabolomics; molecular weight; nonhuman; nuclear magnetic resonance; Saccharomyces cerevisiae Proteins
AbstractThe 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.
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AffiliationNational Research Council Canada (NRC-CNRC); National Institute for Nanotechnology
Peer reviewedYes
NPARC number21270237
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Record identifier4c8aa0fe-5fcd-44e0-bfc9-1b2df4fbab95
Record created2014-01-15
Record modified2016-05-09
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