This article is about the Human Metabolome Database (HMDB.ca). For the Historical Marker Database (HMdb.org), see Historical Marker Database.
The Human Metabolome Database (HMDB)[1][2][3][4] is a comprehensive, high-quality, freely accessible, online database of small moleculemetabolites found in the human body. It bas been created by the Human Metabolome Project funded by Genome Canada[5] and is 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.
Human Metabolome Database
Content
Description
Metabolomics database
Data types captured
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
Every 2 years with monthly corrections and updates
Curation policy
Manually curated
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 5,000 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 ~1,600 drug and drug metabolites, T3DB contains information on 3,100 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.
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] 2017 (version 4.0).[12], 2022 (version 5.0).[11] Details for each of the major HMDB versions (up to version 5.0) is provided in Table 1.
Table 1. Content comparison of HMDB versions
Database Feature or Content Status
HMDB (v1.0)
HMDB (v2.0)
HMDB (v3.0)
HMDB (v4.0)
HMDB (v5.0)
Number of metabolites
2,180
6,408
37,170
114,100
220,945
Number of unique metabolite synonyms
27,700
43,882
152,364
−
−
Number of compounds with disease links
862
1,002
3,948
22,605
22,600
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
72,604
78,841
Number of compounds with experimental reference 1H and or 13C NMR spectra
385
792
1,054
2,801
12,216
Number of compounds with reference MS/MS spectra
390
799
1,249
1,544
4,064
Number of compounds with reference GC-MS reference data
0
279
884
7,418
11,493
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
130
130
'Number of predicted molecular properties
2
2
10
−
−
Scope and accessEdit
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.
^ abcWishart, 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 J.; 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 (January 1, 2007). "HMDB: the Human Metabolobe Database". Nucleic Acids Research. 35 (D1): D521–D526. doi:10.1093/nar/gkl923. PMC1899095. PMID 17202168.
^ abWishart, David S.; Knox, Craig; Guo, An Chi; Eisner, Roman; Young, Nelson; Gautam, Bijaya; Hau, David D.; Psychogios, Nick; Dong, Edison; Bouatra, Souhaila; Mandal, Rupasri; Sinelnikov, Igor; Xia, Jianguo; Jia, Leslie; Cruz, Joseph A.; Lim, Emilia; Sobsey, Constance A.; Shrivastava, Savita; Huang, Paul; Liu, Philip; Fang, Lydia; Peng, Jun; Fradette, Ryan; Cheng, Dean; Tzur, Dan; Clements, Melisa; Lewis, Avalyn; de Souza, Andrea; Zúñiga, Azaret; Dawe, Margot; Xiong, Yeping; Clive, Derrick; Greiner, Russ; Nazyrova, Alsu; Shaykhutdinov, Rustem; Li, Liang; Vogel, Hans J.; Forsythe, Ian J. (1 January 2009). "HMDB: a knowledgebase for the human metabolome". Nucleic Acids Research. 37 (D1): D603–D610. doi:10.1093/nar/gkn810. PMC2686599. PMID 18953024.
^Forsythe, Ian J.; Wishart, David S. (March 1, 2009). "Exploring Human Metabolites Using the Human Metabolome Database". Current Protocols in Bioinformatics. 25: 14.8.1–14.8.45. doi:10.1002/0471250953.bi1408s25. ISBN978-0471250951. PMID 19274632. S2CID 24291704.
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This article is about the Human Metabolome Database HMDB ca For the Historical Marker Database HMdb org see Historical Marker Database 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 It bas been created by the Human Metabolome Project funded by Genome Canada 5 and is 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 Human Metabolome DatabaseContentDescriptionMetabolomics databaseData typescapturedHuman 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 spectraContactResearch centerUniversity of Alberta and The Metabolomics Innovation CentreLaboratoryDavid S WishartPrimary citationHMDB the Human Metabolome Database 1 AccessWebsitehttp www hmdb caDownload URLhttp www hmdb ca downloadsMiscellaneousData releasefrequencyEvery 2 years with monthly corrections and updatesCuration policyManually curatedThe clinical data includes information on gt 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 5 000 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 1 600 drug and drug metabolites T3DB contains information on 3 100 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 Contents 1 Version history 2 Scope and access 3 See also 4 ReferencesVersion history EditThe 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 2017 version 4 0 12 2022 version 5 0 11 Details for each of the major HMDB versions up to version 5 0 is provided in Table 1 Table 1 Content comparison of HMDB versions Database Feature or Content Status HMDB v1 0 HMDB v2 0 HMDB v3 0 HMDB v4 0 HMDB v5 0 Number of metabolites 2 180 6 408 37 170 114 100 220 945Number of unique metabolite synonyms 27 700 43 882 152 364 Number of compounds with disease links 862 1 002 3 948 22 605 22 600Number 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 72 604 78 841Number of compounds with experimental reference 1H and or 13C NMR spectra 385 792 1 054 2 801 12 216Number of compounds with reference MS MS spectra 390 799 1 249 1 544 4 064Number of compounds with reference GC MS reference data 0 279 884 7 418 11 493Number of human specific pathway maps 26 58 442 Number of compounds in Human Metabolome Library 607 920 1 031 Number of HMDB data fields 91 102 114 130 130 Number of predicted molecular properties 2 2 10 Scope and access EditAll 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 EditKEGG DrugBank SMPDB MetaCyc Bovine Metabolome Database Metabolome Metabolomics List of biological databasesReferences Edit a b c 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 J 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 January 1 2007 HMDB the Human Metabolobe Database Nucleic Acids Research 35 D1 D521 D526 doi 10 1093 nar gkl923 PMC 1899095 PMID 17202168 a b Wishart David S Knox Craig Guo An Chi Eisner Roman Young Nelson Gautam Bijaya Hau David D Psychogios Nick Dong Edison Bouatra Souhaila Mandal Rupasri Sinelnikov Igor Xia Jianguo Jia Leslie Cruz Joseph A Lim Emilia Sobsey Constance A Shrivastava Savita Huang Paul Liu Philip Fang Lydia Peng Jun Fradette Ryan Cheng Dean Tzur Dan Clements Melisa Lewis Avalyn de Souza Andrea Zuniga Azaret Dawe Margot Xiong Yeping Clive Derrick Greiner Russ Nazyrova Alsu Shaykhutdinov Rustem Li Liang Vogel Hans J Forsythe Ian J 1 January 2009 HMDB a knowledgebase for the human metabolome Nucleic Acids Research 37 D1 D603 D610 doi 10 1093 nar gkn810 PMC 2686599 PMID 18953024 Forsythe Ian J Wishart David S March 1 2009 Exploring Human Metabolites Using the Human Metabolome Database Current Protocols in Bioinformatics 25 14 8 1 14 8 45 doi 10 1002 0471250953 bi1408s25 ISBN 978 0471250951 PMID 19274632 S2CID 24291704 a b Wishart David S Jewison Timothy Guo An Chi Wilson Michael Knox Craig Liu Yifeng Djombou Feunang Yannick Mandal Rupasri Aziat Farid Dong Edison Bouatra Souhaila Sinelnikov Igor Arndt David Xia Jianguo Liu Philip Yallou Faizath Bjorndahl trent Perez Pineiro Rolando Eisner Roman Allen Felicity Neveu Vanessa Greiner Russ Scalbert Augustin 1 January 2013 HMDB 3 0 The Human Metabolobe Database in 2013 Nucleic Acids Research 41 D1 D801 D807 doi 10 1093 nar gks1065 PMC 3531200 PMID 23161693 a b Human Metabolome Project Retrieved 13 February 2013 Wishart David S Knox Craig Guo An Chi Shrivastava Savita Hassanali Murtaza Stothard Paul Chang Zhan Woolsey Jennifer January 1 2006 DrugBank a comprehensive resource for in silico drug discovery and exploration Nucleic Acids Research 34 D1 D668 D672 doi 10 1093 nar gkj067 PMC 1347430 PMID 16381955 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 6 doi 10 1093 nar gkm958 PMC 2238889 PMID 18048412 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 doi 10 1093 nar gkq1126 PMC 3013709 PMID 21059682 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 doi 10 1093 nar gkp934 PMC 2808899 PMID 19897546 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 doi 10 1093 nar gkp1002 PMC 2808928 PMID 19948758 a b Human Metabolome Database Release Notes Wishart David S Djombou Feunang Yannick Marcu Ana Guo An Chi Liang Kevin Vazquez Fresno Rosa Sajed Tanvir Johnson Daniel Li Carin Karu Naama Sayeeda Zinat Lo Elvis Assempour Nazanin Berjanskii Mark Singhal Sandeep Arndt David Liang Yonjie Badran Hasan Grant Jason Serra Cayuela Arnau Liu Yifeng Mandal Rupa Neveu Vanessa Pon Allison Knox Craig Wilson Michael Manach Claudine Scalbert Augustin 4 January 2018 HMDB 4 0 the human metabolome database for 2018 Nucleic Acids Research 46 D1 D608 D617 doi 10 1093 nar gkx1089 PMC 5753273 PMID 29140435 Retrieved from https en wikipedia org w index php title Human Metabolome Database amp oldid 1162287400, wikipedia, wiki, book, books, library,
