Yeast Metabolome Database

The Yeast Metabolome Database (YMDB) is a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (Baker’s yeast). The YMDB was designed to facilitate yeast metabolomics research, specifically in the areas of general fermentation as well as wine, beer and fermented food analysis. YMDB supports the identification and characterization of yeast metabolites using NMR spectroscopy, GC-MS spectrometry and Liquid chromatography–mass spectrometry (LC-MS spectrometry). The YMDB contains two kinds of data: 1) chemical data and 2) molecular biology/biochemistry data. The chemical data includes 2027 metabolite structures with detailed metabolite descriptions along with nearly 4000 NMR, GC-MS and LC/MS spectra. The Yeast Metabolome Database (YMDB) is a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (Baker’s yeast). The YMDB was designed to facilitate yeast metabolomics research, specifically in the areas of general fermentation as well as wine, beer and fermented food analysis. YMDB supports the identification and characterization of yeast metabolites using NMR spectroscopy, GC-MS spectrometry and Liquid chromatography–mass spectrometry (LC-MS spectrometry). The YMDB contains two kinds of data: 1) chemical data and 2) molecular biology/biochemistry data. The chemical data includes 2027 metabolite structures with detailed metabolite descriptions along with nearly 4000 NMR, GC-MS and LC/MS spectra. The biochemical data includes 1104 protein (and DNA) sequences and more than 900 biochemical reactions (Fig. 1) that are linked to these metabolite entries. Each metabolite entry in the YMDB contains more than 80 data fields with 2/3 of the information being devoted to chemical data and the other 1/3 devoted to enzymatic or biochemical data. Many data fields are hyperlinked to other databases (KEGG, PubChem, MetaCyc, ChEBI, Protein Data Bank, UniProt, and GenBank) and a variety of structure and pathway viewing applets. The YMDB database supports extensive text, sequence, spectral, chemical structure and relational query searches.