HMDB: the Human Metabolome Database

TLDR

The Human Metabolome Database (HMDB) is the most comprehensive curated collection of human metabolites and metabolic data worldwide. It was created to serve biochemists, clinical chemists, physicians, medical geneticists, nutritionists, and the broader metabolomics community. HMDB contains over 2,180 endogenous metabolite records compiled from literature, experimental MS and NMR concentration data from urine, blood, and cerebrospinal fluid, purified metabolite spectra, and provides ~90 data fields per entry plus extensive search, query, and browsing tools. The database is available at the author’s webpage.

Abstract

The Human Metabolome Database (HMDB) is currently the most complete and comprehensive curated collection of human metabolite and human metabolism data in the world. It contains records for more than 2180 endogenous metabolites with information gathered from thousands of books, journal articles and electronic databases. In addition to its comprehensive literature-derived data, the HMDB also contains an extensive collection of experimental metabolite concentration data compiled from hundreds of mass spectra (MS) and Nuclear Magnetic resonance (NMR) metabolomic analyses performed on urine, blood and cerebrospinal fluid samples. This is further supplemented with thousands of NMR and MS spectra collected on purified, reference metabolites. Each metabolite entry in the HMDB contains an average of 90 separate data fields including a comprehensive compound description, names and synonyms, structural information, physico-chemical data, reference NMR and MS spectra, biofluid concentrations, disease associations, pathway information, enzyme data, gene sequence data, SNP and mutation data as well as extensive links to images, references and other public databases. Extensive searching, relational querying and data browsing tools are also provided. The HMDB is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community. The HMDB is available at: Author Webpage