Yeast Metabolome Database

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Yeast Metabolome Database
Content
DescriptionMetabolomics database
Data types
captured		Yeast metabolite structures, metabolite descriptions, metabolite reactions, metabolite enzymes and transporters, yeast enzyme and transporter sequences, chemical properties, nomenclature, synonyms, chemical taxonomy, metabolite NMR spectra, metabolite GC-MS spectra, metabolite LC-MS spectra
Contact
Research center
University of Alberta and The Metabolomics Innovation Centre
LaboratoryDavid S. Wishart
Primary citationThe Yeast Metabolome Database.[1]
Access
Websitehttp://www.ymdb.ca
Download URLhttp://www.ymdb.ca/downloads
Miscellaneous
Data release
frequency		Every 2-3 years with periodic corrections and updates
Curation policyManually curated

The Yeast Metabolome Database (YMDB)

LC/MS
spectra.

The biochemical data includes 1104

biochemical reactions (Fig. 1) that are linked to these metabolite entries.[1] 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.

Scope and access

All data in YMDB is non-proprietary or is derived from a non-proprietary source. It is freely accessible and available to anyone. In addition, nearly every data item is fully traceable and explicitly referenced to the original source. YMDB data is available through a public web interface and downloads.

Users may search through the YMDB using a variety of database-specific tools. The simple text query supports general text queries of the textual component of the database. By selecting either metabolites or proteins in the “search for” field it is possible to restrict the search and the returned results to only those data associated with metabolites or with proteins. YMDB’s browse tool generates a tabular synopsis of YMDB's content (Fig. 2). This browser view allows users to casually scroll through the database or re-sort its contents. Clicking on a given MetaboCard button brings up the full data content for the corresponding metabolite (Fig. 3). Under the Search link users will find a number of search options listed in a pull-down menu. The Chem Query option allows users to draw (using MarvinSketch applet or a ChemSketch applet) or to type (

NMR Spectra Search links. Users may download YMDB’s complete textual data, chemical structures
and sequence data by clicking on the Download button.

See also

References

  1. ^
    PMID 22064855
    .

External links
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