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YMDB Version 2.0


The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast). This database covers metabolites described in textbooks, scientific journals, metabolic reconstructions and other electronic databases. YMDB contains metabolites arising from normal S. cerevisiae metabolism under defined laboratory conditions as well as metabolites generated by S. cerevisiae when used in baking and in the production of wines, beers and spirits. YMDB currently contains 16042 small molecules with 909 associated enzymes and 149 associated transporters. Each small molecule has 48 data fields describing the metabolite, its chemical properties and links to spectral and chemical databases. Each enzyme/transporter is linked to its associated metabolites and has 30 data fields describing both the gene and corresponding protein.

Citing the Yeast Metabolome Database:

  • YMDB 2.0: A Significantly Expanded Version of the Yeast Metabolome Database. Ramirez-Guana M, Marcu A, Pon A, Guo AC, Sajed T, Wishart NA, Karu N, Djoumbou Y, Arndt D and Wishart DS. Nucleic Acids Res. 2017 Jan 4;45(D1):D440-D445. PubMed: 27899612
  • YMDB: The Yeast Metabolome Database. Jewison T, Neveu V, Lee J, Knox C, Liu P, Mandal R, Murthy RK, Sinelnikov I, Guo AC, Wilson M, Djoumbou Y and Wishart DS. Nucleic Acids Res. 2012 Jan;40(Database ussue):D815-20. PubMed: 22064855