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Welcome to HMDB Version 4.0
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 applitions in metabolomics, clinil chemistry, biomarker discovery and general edution. The database is designed to contain or link three kinds of data: 1) chemil data, 2) clinil data, and 3) molecular biology/biochemistry data. The database contains 114,184 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, 5,702 protein sequences are linked to these metabolite entries. Each Metabord entry contains 130 data fields with 2/3 of the information being devoted to chemil/clinil data and the other 1/3 devoted to enzymatic or biochemil 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, chemil 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 ~2280 drug and drug metabolites, T3DB contains information on ~3670 common toxins and environmental pollutants, SMPDB contains pathway diagrams for ~25,000 human metabolic and disease pathways, while FooDB contains equivalent information on ~28,000 food components and food additives.

Citing the Human Metabolome Database:

  1. Wishart DS, Tzur D, Knox C, et al., HMDB: the Human Metabolome Database. Nucleic Acids Res. 2007 Jan;35(Database issue):D521-6. 17202168
  2. Wishart DS, Knox C, Guo AC, et al., HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res. 2009 37(Database issue):D603-610. 18953024
  3. 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. 23161693
  4. Wishart DS, Feunang YD, Marcu A, Guo AC, Liang K, et al., HMDB 4.0 — The Human Metabolome Database for 2018. Nucleic Acids Res. 2018. Jan 4;46(D1):D608-17. 29140435