Human Metabolome Database

Last updated
Human Metabolome Database
Human Metabolome Database logo.png
Content
DescriptionMetabolomics 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
Contact
Research center University of Alberta and The Metabolomics Innovation Centre
Laboratory David S. Wishart
Primary citationHMDB: the Human Metabolome Database. [1]
Access
Website http://www.hmdb.ca
Download URL http://www.hmdb.ca/downloads
Miscellaneous
Data release
frequency		Every 2 years with monthly corrections and updates
Curation policyManually curated

The Human Metabolome Database (HMDB) [1] [2] [3] [4] is a comprehensive online database of small molecule metabolites found in the human body. It has 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.

Contents

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] toxin database, [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.

Version history

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 StatusHMDB (v1.0)HMDB (v2.0)HMDB (v3.0)HMDB (v4.0)HMDB (v5.0)
Number of metabolites2,1806,40837,170114,100220,945
Number of unique metabolite synonyms27,70043,882152,364−−
Number of compounds with disease links8621,0023,94822,60522,600
Number of compounds with biofluid or tissue concentration data8834,4136,796−−
Number of compounds with chemical synthesis references2201,6478,86372,60478,841
Number of compounds with experimental reference 1H and or 13C NMR spectra3857921,0542,80112,216
Number of compounds with reference MS/MS spectra3907991,2491,5444,064
Number of compounds with reference GC-MS reference data02798847,41811,493
Number of human-specific pathway maps2658442−−
Number of compounds in Human Metabolome Library6079201,031−−
Number of HMDB data fields91102114130130
Number of predicted molecular properties2210−−

Scope and access

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

References

  1. 1 2 3 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.
  2. 1 2 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; 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. PMC   2686599 . PMID   18953024.
  3. ↑ 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.
  4. 1 2 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; Pérez Piñeiro, 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.
  5. 1 2 "Human Metabolome Project" . Retrieved 13 February 2013.
  6. ↑ 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.
  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): D901-6. doi:10.1093/nar/gkm958. PMC   2238889 . PMID   18048412.
  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. doi:10.1093/nar/gkq1126. PMC   3013709 . PMID   21059682.
  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. doi:10.1093/nar/gkp934. PMC   2808899 . PMID   19897546.
  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. doi:10.1093/nar/gkp1002. PMC   2808928 . PMID   19948758.
  11. 1 2 "Human Metabolome Database Release Notes".
  12. ↑ Wishart, David S.; Djombou Feunang, Yannick; Marcu, Ana; Guo, An Chi; Liang, Kevin; Vázquez 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.
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