The Human Metabolome Database (HMDB) is a comprehensive resource providing information on the human metabolome. Since its initial release in 2007, HMDB has been used in nearly 1000 published studies in metabolomics, clinical biochemistry, and systems biology. The latest release, version 3.0, has significantly expanded and enhanced the database. The number of annotated metabolite entries has increased from 6500 to over 40000, a 600% increase. This expansion includes both 'detected' metabolites (those with measured concentrations or experimental confirmation) and 'expected' metabolites (those for which biochemical pathways are known or human intake is frequent but have not yet been detected). The database now contains more metabolites with biofluid or tissue concentration data, more compounds with reference spectra, and more data fields per entry. New database visualization tools and data content have been added or enhanced, including better spectral viewing tools, more powerful chemical substructure searches, an improved chemical taxonomy, and better, more interactive pathway maps. The HMDB has been expanded to include more detailed information on metabolites, including their chemical taxonomy, origin, biofunction, application, and cellular location. The database now includes data on metabolite transporters, channels, and symporters. The HMDB has also significantly increased the number and quality of reference nuclear magnetic resonance (NMR), tandem mass spectrometry (MS/MS), and gas chromatography-mass spectrometry (GC-MS) spectra. The HMDB now has 442 hand-drawn, zoomable, fully hyperlinked human metabolic pathway maps, increasing the total number of pathway diagrams by 800%. The HMDB's chemical taxonomy has been completely redone to be more standardized and self-consistent. The HMDB also has a chemical ontology that includes status, origin, biofunction, application, and cellular location. The HMDB's user interface has been improved, with the MetaboCard now divided into 14 distinctive categories or superfields. The HMDB has also added a Protein Browse option, allowing users to browse through, view, or sort the list of human proteins, enzymes, and transporters associated with each metabolite. The HMDB's spectral databases and spectral searching tools have been enhanced, allowing users to select between expected, detected, or combined metabolites for their MS search routines. The HMDB's data formats and data structures have also been improved, with all structure information consolidated into a central chemical structure database (MolDB) and all spectral information into a central spectral structure database (SpecDB). The HMDB's data has also been converted to an easily parsed XML format, making data downloads and development of data extraction routines much simpler and faster. The HMDB is a comprehensive, web-accessible metabolomics database that brings together quantitative chemical, physical, clinical, and biological data about allThe Human Metabolome Database (HMDB) is a comprehensive resource providing information on the human metabolome. Since its initial release in 2007, HMDB has been used in nearly 1000 published studies in metabolomics, clinical biochemistry, and systems biology. The latest release, version 3.0, has significantly expanded and enhanced the database. The number of annotated metabolite entries has increased from 6500 to over 40000, a 600% increase. This expansion includes both 'detected' metabolites (those with measured concentrations or experimental confirmation) and 'expected' metabolites (those for which biochemical pathways are known or human intake is frequent but have not yet been detected). The database now contains more metabolites with biofluid or tissue concentration data, more compounds with reference spectra, and more data fields per entry. New database visualization tools and data content have been added or enhanced, including better spectral viewing tools, more powerful chemical substructure searches, an improved chemical taxonomy, and better, more interactive pathway maps. The HMDB has been expanded to include more detailed information on metabolites, including their chemical taxonomy, origin, biofunction, application, and cellular location. The database now includes data on metabolite transporters, channels, and symporters. The HMDB has also significantly increased the number and quality of reference nuclear magnetic resonance (NMR), tandem mass spectrometry (MS/MS), and gas chromatography-mass spectrometry (GC-MS) spectra. The HMDB now has 442 hand-drawn, zoomable, fully hyperlinked human metabolic pathway maps, increasing the total number of pathway diagrams by 800%. The HMDB's chemical taxonomy has been completely redone to be more standardized and self-consistent. The HMDB also has a chemical ontology that includes status, origin, biofunction, application, and cellular location. The HMDB's user interface has been improved, with the MetaboCard now divided into 14 distinctive categories or superfields. The HMDB has also added a Protein Browse option, allowing users to browse through, view, or sort the list of human proteins, enzymes, and transporters associated with each metabolite. The HMDB's spectral databases and spectral searching tools have been enhanced, allowing users to select between expected, detected, or combined metabolites for their MS search routines. The HMDB's data formats and data structures have also been improved, with all structure information consolidated into a central chemical structure database (MolDB) and all spectral information into a central spectral structure database (SpecDB). The HMDB's data has also been converted to an easily parsed XML format, making data downloads and development of data extraction routines much simpler and faster. The HMDB is a comprehensive, web-accessible metabolomics database that brings together quantitative chemical, physical, clinical, and biological data about all