Human Metabolome Database

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Human Metabolome Database
Human Metabolome Database logo.png
Description Metabolomics database
Data types
Human metabolite structures, metabolite descriptions, metabolite reactions, metabolite enzymes and transporters, human enzyme and transporter sequences, human metabolic pathways, normal and abnormal metabolite concentrations in humans, associated diseases, chemical properties, nomenclature, synonyms, chemical taxonomy, metabolite NMR spectra, metabolite GC-MS spectra, metabolite LC-MS spectra
Research center University of Alberta and The Metabolomics Innovation Centre
Laboratory Dr. David Wishart
Primary citation HMDB: the Human Metabolome Database.[1]
Download URL
Data release
Every 2 years with monthly corrections and updates
Curation policy Manually curated

The Human Metabolome Database (HMDB)[1][2][3][4] is a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in the human body. Created by the Human Metabolome Project funded by Genome Canada.[5] One of the first dedicated metabolomics databases, the HMDB facilitates human metabolomics research, including the identification and characterization of human metabolites using NMR spectroscopy, GC-MS spectrometry and LC/MS spectrometry. To aid in this discovery process, the HMDB contains three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular biology/biochemistry data (Fig. 1-3). The chemical data includes 41,514 metabolite structures with detailed descriptions along with nearly 10,000 NMR, GC-MS and LC/MS spectra.

Fig. 1. HMDB metabolite
Fig. 2. HMDB metabolite chemical and physical information
Fig. 3. HMDB metabolite clinical information

The clinical data includes information on >10,000 metabolite-biofluid concentrations and metabolite concentration information on more than 600 different human diseases. The biochemical data includes 5,688 protein (and DNA) sequences and more than 5000 biochemical reactions that are linked to these metabolite entries.[5] Each metabolite entry in the HMDB 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, MetaCyc, PubChem, Protein Data Bank, ChEBI, Swiss-Prot, and GenBank) and a variety of structure and pathway viewing applets. The HMDB database supports extensive text, sequence, spectral, chemical structure and relational query searches. It has been widely used in metabolomics, clinical chemistry, biomarker discovery and general biochemistry education.

Four additional databases, DrugBank,[6][7][8] T3DB,[9] SMPDB [10] 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 700 human metabolic and disease pathways, while FooDB contains equivalent information on ~28,000 food components and food additives.

Version history[edit]

The first version of HMDB was released on January 1, 2007,[1] followed by two subsequent versions on January 1, 2009 (version 2.0),[2] August 1, 2009 (version 2.5), September 18, 2012 (version 3.0)[4] and Jan. 1, 2013 (version 3.5).[11] Details for each of the major HMDB versions (up to version 3.0) is provided in Table 1.

Table 1. Content comparison of HMDB 1.0 with HMDB 2.0 and HMDB 3.0
Database Feature or Content Status HMDB (v1.0) HMDB (v2.0) HMDB (v3.0)
Number of metabolites 2,180 6,408 37,170
Number of unique metabolite synonyms 27,700 43,882 152,364
Number of compounds with disease links 862 1,002 3,948
Number of compounds with biofluid or tissue concentration data 883 4,413 6,796
Number of compounds with chemical synthesis references 220 1,647 8,863
Number of compounds with experimental reference 1H and or 13C NMR spectra 385 792 1,054
Number of compounds with reference MS/MS spectra 390 799 1,249
Number of compounds with reference GC-MS reference data 0 279 884
Number of human-specific pathway maps 26 58 442
Number of compounds in Human Metabolome Library 607 920 1,031
Number of HMDB data fields 91 102 114
'Number of predicted molecular properties 2 2 10

Scope and access[edit]

All data in HMDB is non-proprietary or is derived from a non-proprietary source. It is freely accessible and available to anyone. In addition, nearly every data item is fully traceable and explicitly referenced to the original source. HMDB data is available through a public web interface and downloads.

See also[edit]


  1. ^ a b c Wishart, DS; Tzur, D; Knox, C; Eisner, R; Guo, AC; Young, N; Cheng, D; Jewell, K; Arndt, D; Sawhney, S; Fung, C; Nikolai, L; Lewis, M; Coutouly, MA; Forsythe, I; Tang, P; Shrivastava, S; Jeroncic, K; Stothard, P; Amegbey, G; Block, D; Hau, DD; Wagner, J; Miniaci, J; Clements, M; Gebremedhin, M; Guo, N; Zhang, Y; Duggan, GE; Macinnis, GD; Weljie, AM; Dowlatabadi, R; Bamforth, F; Clive, D; Greiner, R; Li, L; Marrie, T; Sykes, BD; Vogel, HJ; Querengesser, L (Jan 2007). "HMDB: the Human Metabolome Database.". Nucleic Acids Research. 35 (Database issue): D521–6. PMC 1899095Freely accessible. PMID 17202168. doi:10.1093/nar/gkl923. 
  2. ^ a b Wishart, DS; Knox, C; Guo, AC; Eisner, R; Young, N; Gautam, B; Hau, DD; Psychogios, N; Dong, E; Bouatra, S; Mandal, R; Sinelnikov, I; Xia, J; Jia, L; Cruz, JA; Lim, E; Sobsey, CA; Shrivastava, S; Huang, P; Liu, P; Fang, L; Peng, J; Fradette, R; Cheng, D; Tzur, D; Clements, M; Lewis, A; De Souza, A; Zuniga, A; Dawe, M; Xiong, Y; Clive, D; Greiner, R; Nazyrova, A; Shaykhutdinov, R; Li, L; Vogel, HJ; Forsythe, I (Jan 2009). "HMDB: a knowledgebase for the human metabolome". Nucleic Acids Research. 37 (Database issue): D603–10. PMC 2686599Freely accessible. PMID 18953024. doi:10.1093/nar/gkn810. 
  3. ^ Forsythe, IJ; Wishart, DS (Mar 2009). "Exploring human metabolites using the human metabolome database". Current Protocols in Bioinformatics. Chapter 14: Unit14.8. ISBN 0471250953. PMID 19274632. doi:10.1002/0471250953.bi1408s25. 
  4. ^ a b Wishart, DS; Jewison, T; Guo, AC; Wilson, M; Knox, C; Liu, Y; Djoumbou, Y; Mandal, R; Aziat, F; Dong, E; Bouatra, S; Sinelnikov, I; Arndt, D; Xia, J; Liu, P; Yallou, F; Bjorndahl, T; Perez-Pineiro, R; Eisner, R; Allen, F; Neveu, V; Greiner, R; Scalbert, A (Jan 2013). "HMDB 3.0--The Human Metabolome Database in 2013". Nucleic Acids Research. 41 (Database issue): D801–7. PMC 3531200Freely accessible. PMID 23161693. doi:10.1093/nar/gks1065. 
  5. ^ a b "Human Metabolome Project". Retrieved 13 February 2013. 
  6. ^ Wishart, DS; Knox C; Guo AC; et al. (Jan 2006). "DrugBank: a comprehensive resource for in silico drug discovery and exploration". Nucleic Acids Research. 34 (Database issue): D668-D672. PMC 1347430Freely accessible. PMID 16381955. doi:10.1093/nar/gkj067. 
  7. ^ Wishart, DS; Knox C; Guo AC; et al. (Jan 2008). "DrugBank: a knowledgebase for drugs, drug actions and drug targets". Nucleic Acids Research. 36 (Database issue): D901–906. PMC 2238889Freely accessible. PMID 18048412. doi:10.1093/nar/gkm958. 
  8. ^ Knox, C; Law, V; Jewison, T; Liu, P; Ly, S; Frolkis, A; Pon, A; Banco, K; Mak, C; Neveu, V; Djoumbou, Y; Eisner, R; Guo, AC; Wishart, DS. (Jan 2011). "DrugBank 3.0: a comprehensive resource for 'omics' research on drugs.". Nucleic Acids Research. 39 (Database issue): D1035–41. PMC 3013709Freely accessible. PMID 21059682. doi:10.1093/nar/gkq1126. 
  9. ^ Lim, E; Pon A; Djoumbou Y; Knox C; Shrivastava S; Guo AC; Neveu V; Wishart DS. (Jan 2010). "T3DB: a comprehensively annotated database of common toxins and their targets.". Nucleic Acids Research. 38 (Database issue): D781-6. PMC 2808899Freely accessible. PMID 19897546. doi:10.1093/nar/gkp934. 
  10. ^ Frolkis, A; Knox, C; Lim, E; Jewison, T; Law, V; Hau, DD; Liu, P; Gautam, B; Ly, S; Guo, AC; Xia, J; Liang, Y; Shrivastava, S; Wishart, DS. (Jan 2010). "SMPDB: The Small Molecule Pathway Database.". Nucleic Acids Research. 38 (Database issue): D480–7. PMC 2808928Freely accessible. PMID 19948758. doi:10.1093/nar/gkp1002. 
  11. ^ "Human Metabolome Database Release Notes".