HMDB: the Human Metabolome Database
- David S. Wishart, Departments of Computing Science and Biology, University of Alberta
- Dan Tzur
- Craig Knox
- Roman Eisner
- An Chi Guo
- Nelson Young
- Dean Cheng
- Kevin Jewell, Alberta Ingenuity
- David Arndt
- Summit Sawhney, Department of Biological Sciences, University of Alberta
- Chris Fung, Department of Biological Sciences, University of Alberta
- Lisa Nikolai
- Mike Lewis
- Marie-Aude Coutouly
- Ian Forsythe
- Peter Tang
- Savita Shrivastava
- Kevin Jeroncic
- Paul Stothard, Department of Agricultural, Food and Nutritional Science (AFNS)
- Godwin Amegbey
- David Block
- David D. Hau
- James Wagner, Department of Computing Science, University of Alberta
- Jessica Miniaci, Department of Biochemistry, University of Alberta
- Melisa Clements, Department of Chemistry, University of Alberta
- Mulu Gebremedhin, Department of Chemistry, University of Alberta
- Natalie Guo, Department of Chemistry, University of Alberta
- Ying Zhang, Department of Chemistry, University of Alberta
- Gavin E. Duggan, Department of Biological Sciences, University of Calgary
- Glen D. MacInnis, Department of Biological Sciences, University of Calgary
- Alim M. Weljie, Department of Biological Sciences, University of Calgary
- Reza Dowlatabadi, Department of Biological Sciences, University of Calgary
- Fiona Bamforth, Department of Medicine, University of Alberta
- Derrick Clive, Department of Chemistry, University of Alberta
- Russ Greiner, Dept of Computing Science; PI of AICML
- Liang Li, Department of Chemistry, University of Alberta
- Tom Marrie, Department of Medicine, University of Alberta
- Brian D. Sykes, Department of Biochemistry, University of Alberta
- Hans J. Vogel, Department of Biological Sciences, University of Calgary
- Lori Querengesser, Department of Computing Science, University of Alberta
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: www.hmdb.ca
Citation
D. Wishart, D. Tzur, C. Knox, R. Eisner, A. Guo, N. Young, D. Cheng, K. Jewell, D. Arndt, S. Sawhney, C. Fung, L. Nikolai, M. Lewis, M. Coutouly, I. Forsythe, P. Tang, S. Shrivastava, K. Jeroncic, P. Stothard, G. Amegbey, D. Block, D. Hau, J. Wagner, J. Miniaci, M. Clements, M. Gebremedhin, N. Guo, Y. Zhang, G. Duggan, G. MacInnis, A. Weljie, R. Dowlatabadi, F. Bamforth, D. Clive, R. Greiner, L. Li, T. Marrie, B. Sykes, H. Vogel, L. Querengesser. "HMDB: the Human Metabolome Database". Nucleic Acids Research (NAR), 35, pp D521 -- D526, January 2007.| Keywords: | human metabolome, database, machine learning, bioinformatics, hmp, bioinformatics, medical informatics, metabolomics |
| Category: | In Journal |
BibTeX
@article{Wishart+al:NAR07,
author = {David S. Wishart and Dan Tzur and Craig Knox and Roman Eisner and
An Chi Guo and Nelson Young and Dean Cheng and Kevin Jewell and David Arndt
and Summit Sawhney and Chris Fung and Lisa Nikolai and Mike Lewis and
Marie-Aude Coutouly and Ian Forsythe and Peter Tang and Savita Shrivastava
and Kevin Jeroncic and Paul Stothard and Godwin Amegbey and David Block and
David D. Hau and James Wagner and Jessica Miniaci and Melisa Clements and
Mulu Gebremedhin and Natalie Guo and Ying Zhang and Gavin E. Duggan and
Glen D. MacInnis and Alim M. Weljie and Reza Dowlatabadi and Fiona Bamforth
and Derrick Clive and Russ Greiner and Liang Li and Tom Marrie and Brian D.
Sykes and Hans J. Vogel and Lori Querengesser},
title = {HMDB: the Human Metabolome Database},
Volume = "35",
Pages = {D521 -- D526},
journal = {Nucleic Acids Research (NAR)},
year = 2007,
}Last Updated: September 21, 2012Submitted by Russ Greiner
