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HMDB: The human metabolome database Open Access


Author or creator
Wishart, David S.
Tzur, Dan
Knox, Craig
Eisner, Roman
Guo, An Chi
Young, Nelson
Cheng, Dean
Jewell, Kevin
Arndt, David
Sawhney, Summit
Fung, Chris
Nikolai, Lisa
Lewis, Mike
Coutouly, Marie-Aude
Forsythe, Ian
Tang, Peter
Shrivastava, Savita
Jeroncic, Kevin
Stothard, Paul
Amegbey, Godwin
Block, David
Hau, David D.
Wagner, James
Miniaci, Jessica
Melisa, Gebremedhin
Mulu, Guo
Natalie, Zhang
Ying, Duggan
Gavin E.
Macinnis, Glen D.
Weljie, Alim M.
Dowlatabadi, Reza
Bamforth, Fiona
Clive, Derrick
Greiner, Russ
Li, Liang
Marrie, Tom
Sykes, Brian D.
Vogel, Hans J.
Querengesser, Lori
Additional contributors
Type of item
Journal Article (Published)
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:

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Attribution-NonCommercial 2.0 International
Citation for previous publication
Wishart, David S., Tzur, Dan, Knox, Craig, Eisner, Roman, Guo, An Chi, Young, Nelson, Cheng, Dean, Jewell, Kevin, Arndt, David, Sawhney, Summit, Fung, Chris, Nikolai, Lisa, Lewis, Mike, Coutouly, Marie-Aude, Forsythe, Ian, Tang, Peter, Shrivastava, Savita, Jeroncic, Kevin, Stothard, Paul, Amegbey, Godwin, Block, David, Hau, David D., Wagner, James, Miniaci, Jessica, Clements, Melisa, Gebremedhin, Mulu, Guo, Natalie, Zhang, Ying, Duggan, Gavin E., Macinnis, Glen D., Weljie, Alim M., Dowlatabadi, Reza, Bamforth, Fiona, Clive, Derrick, Greiner, Russ, Li, Liang, Marrie, Tom, Sykes, Brian D., Vogel, Hans J., & Querengesser, Lori. (2007). HMDB: The human metabolome database. Nucleic Acids Research, 35(Suppl. 1), D521-D526.


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