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 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.
 | |
| 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 |
| Contact | |
| Research center | University of Alberta and The Metabolomics Innovation Centre |
| Laboratory | David S. Wishart |
| Primary citation | HMDB: 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 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.
Version 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.
| 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 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
editReferences
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; 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.
- ^ 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; 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.
- ^ 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; 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.