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 3.5) contains 41,514 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, 5,688 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, UniProt, 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 ~1600 drug and drug metabolites, T3DB contains information on 3100 common toxins and environmental pollutants, SMPDB contains pathway diagrams for 440 human metabolic and disease pathways, while FooDB contains equivalent information on ~28,000 food components and food additives.
HMDB is supported by David Wishart,
Departments of Computing Science &
University of Alberta.
HMDB is also supported by The Metabolomics Innovation Centre, a Genome Canada-funded core
facility serving the scientific community and industry with world-class expertise and cutting-edge technologies in metabolomics.
Citing the HMDB
HMDB is offered to the public as a freely available resource. Use and re-distribution of the data, in whole or in part,
for commercial purposes requires explicit permission of the authors and explicit acknowledgment of the source material (HMDB)
and the original publication (see below). We ask that users who download significant portions of the database cite the HMDB
paper in any resulting publications.
- Wishart DS, Tzur D, Knox C, et al.,
HMDB: the Human Metabolome Database.
Nucleic Acids Res. 2007 Jan;35(Database issue):D521-6.
- Wishart DS, Knox C, Guo AC, et al.,
HMDB: a knowledgebase for the human metabolome.
Nucleic Acids Res. 2009 37(Database issue):D603-610.
- Wishart DS, Jewison T, Guo AC, Wilson M, Knox C, et al.,
HMDB 3.0—The Human Metabolome Database in 2013.
Nucleic Acids Res. 2013. Jan 1;41(D1):D801-7.