HMDB 4.0: the human metabolome database for 2018

TLDR

HMDB is a comprehensive, web‑enabled database of human metabolites that catalogs their biological roles, concentrations, disease links, reactions, pathways, and spectra, and has become the standard resource for metabolomics research since 2007. The 4.0 update adds extensive predicted MS/MS and GC‑MS reference spectra and physiologically feasible metabolite structures to support novel metabolite identification. HMDB 4.0 represents the most substantial upgrade to date, tripling annotated metabolites, quadrupling experimental spectra, expanding pathways 60‑fold, and enhancing taxonomy, ontology, search tools, metabolite‑SNP interactions, drug effects, and overall site performance for broad scientific use.

Abstract

The Human Metabolome Database or HMDB (www.hmdb.ca) is a web-enabled metabolomic database containing comprehensive information about human metabolites along with their biological roles, physiological concentrations, disease associations, chemical reactions, metabolic pathways, and reference spectra. First described in 2007, the HMDB is now considered the standard metabolomic resource for human metabolic studies. Over the past decade the HMDB has continued to grow and evolve in response to emerging needs for metabolomics researchers and continuing changes in web standards. This year's update, HMDB 4.0, represents the most significant upgrade to the database in its history. For instance, the number of fully annotated metabolites has increased by nearly threefold, the number of experimental spectra has grown by almost fourfold and the number of illustrated metabolic pathways has grown by a factor of almost 60. Significant improvements have also been made to the HMDB's chemical taxonomy, chemical ontology, spectral viewing, and spectral/text searching tools. A great deal of brand new data has also been added to HMDB 4.0. This includes large quantities of predicted MS/MS and GC-MS reference spectral data as well as predicted (physiologically feasible) metabolite structures to facilitate novel metabolite identification. Additional information on metabolite-SNP interactions and the influence of drugs on metabolite levels (pharmacometabolomics) has also been added. Many other important improvements in the content, the interface, and the performance of the HMDB website have been made and these should greatly enhance its ease of use and its potential applications in nutrition, biochemistry, clinical chemistry, clinical genetics, medicine, and metabolomics science.