The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. It is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education. The database is designed to contain or link three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular biology/biochemistry data. The database (version 2.5) contains over 7900 metabolite entries including both water-soluble and lipid soluble metabolites as well as metabolites that would be regarded as either abundant (> 1 uM) or relatively rare (< 1 nM). Additionally, approximately 7200 protein (and DNA) sequences are linked to these metabolite entries. Each MetaboCard entry contains more than 110 data fields with 2/3 of the information being devoted to chemical/clinical data and the other 1/3 devoted to enzymatic or biochemical data. Many data fields are hyperlinked to other databases (KEGG, PubChem, MetaCyc, ChEBI, PDB, Swiss-Prot, and GenBank) and a variety of structure and pathway viewing applets. The HMDB database supports extensive text, sequence, chemical structure and relational query searches. Four additional databases, DrugBank, T3DB, SMPDB and FooDB are also part of the HMDB suite of databases. DrugBank contains equivalent information on ~1500 drugs, T3DB contains information on 2900 common toxins and environmental pollutants, SMPDB contains pathway diagrams for 350 human metabolic and disease pathways, while FooDB contains equivalent information on ~2000 food components and food additives.
HMDB is supported by David Wishart, Departments of Computing Science & Biological Sciences, University of Alberta.
The simple text query (above) supports general text queries of the entire textual component of the database. Clicking on the Browse button (on the HMDB navigation panel above) generates a tabular synopsis of the HMDB's content. This browse 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. The Biofluids button generates hyperlinked tables listing normal and abnormal concentrations of different metabolites for 7 different biofluids. The ChemQuery button allows users to draw (using a ChemSketch applet) or write (using a SMILES string) a chemical compound and to search HMDB for chemicals similar or identical to the query compound. The TextQuery button supports a more sophisticated text search (partial word matches, case sensitive, misspellings, etc.) of the text portion of HMDB. The SeqSearch button allows users to conduct BLAST sequence searches of the 5500 sequences contained in HMDB. Both single and multiple sequence BLAST queries are supported. The DataExtractor button opens an easy-to-use relational query search tool that allows users to select or search over various combinations of subfields. The DataExtractor is the most sophisticated search tool for HMDB. The MS Search allows users to submit Mass spectral files (MoverZ format) that will be searched against the HMDB's library of MS/MS spectra. This allows the identification of metabolites from mixtures via MS/MS spectroscopy. The NMR Search allows users to submit peak lists from 1H or 13C NMR spectra (both pure and mixtures) and to have these peak lists compared to the NMR libraries contained in the HMDB. This allows the identification of metabolites from mixtures via NMR spectroscopy. The Download button provides links to collected sequence, image and text files associated with the HMDB. The HML Home button links to the Human Metabolome Library (HML) home page. The HML lists metabolites that can be ordered for a fee by researchers around the world. The Explain button lists statistics and source data used to assemble the HMDB.
