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Human Metabolome Database information


Human Metabolome Database
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 centerUniversity of Alberta and The Metabolomics Innovation Centre
LaboratoryDavid S. Wishart
Primary citationHMDB: the Human Metabolome Database.[1]
Access
Websitehttp://www.hmdb.ca
Download URLhttp://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, 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.

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.

  1. ^ a b 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. ^ 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. ^ 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. ^ a b "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.

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Human Metabolome Database

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The Human Metabolome Database (HMDB) is a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in the human...

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Metabolome

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biofluid-specific metabolome databases. Some of the better known metabolome databases include the Human Metabolome Database or HMDB, the Yeast Metabolome Database or...

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Golm Metabolome Database

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The Golm Metabolome Database (GMD) is a gas chromatography (GC) – mass spectrometry (MS) reference library dedicated to metabolite profiling experiments...

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Serum Metabolome Database

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Serum Metabolome database is a free web database about small molecule metabolites found in human serum and their concentration values. The database includes...

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Allura Red AC

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doi:10.1021/ed100545v. "Human Metabolome Database: Showing metabocard for Allura red AC (HMDB0032884)". Human Metabolome Database. 11 September 2012. Retrieved...

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Metabolomics

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draft of the human metabolome. The Human Metabolome Database (HMDB) is perhaps the most extensive public metabolomic spectral database to date and is...

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Small Molecule Pathway Database

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suite of metabolomics databases that also includes Human Metabolome Database, DrugBank, and the Toxin and Toxin-Target Database (T3DB). While DrugBank...

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List of chemical databases

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www.emolecules.com. Retrieved 2020-07-27. "Human Metabolome Database: About the Human Metabolome Database". hmdb.ca. Retrieved 2020-07-27. Van Santen...

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Urolithin A

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Chromatography A. 1428: 162–75. doi:10.1016/j.chroma.2015.08.044. PMID 26341594. Urolithin A at Phenol-Explorer.eu Urolithin A at the Human Metabolome Database...

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Pyrroloquinoline quinone

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Retrieved 18 July 2015. "Pyrroloquinoline quinone (HMDB13636)". Human Metabolome Database. University of Alberta. Retrieved 19 July 2015, citing: PMID 2558842:...

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Phosphocreatine

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(1686): 401–403. Bibcode:1927Sci....65..401F. doi:10.1126/science.65.1686.401. PMID 17807679. Human Metabolome Database at the University of Alberta...

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Human microbiome

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sporogenes. IPA metabolism diagram "3-Indolepropionic acid". Human Metabolome Database. University of Alberta. Retrieved 12 June 2018. Chyan YJ, Poeggeler...

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Gut microbiota

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sporogenes. IPA metabolism diagram "3-Indolepropionic acid". Human Metabolome Database. University of Alberta. Retrieved 12 June 2018. Chyan YJ, Poeggeler...

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Carboxylic acid

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pp. 5–94 to 5–98. ISBN 978-1439855119. "Chlorocarbonic acid". Human Metabolome Database. Smith, Brian. "The C=O Bond, Part VIII: Review". Spectroscopy...

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Ergothioneine

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Chemistry. 285 (24): 18134–8. doi:10.1074/jbc.C110.106377. PMC 2881734. PMID 20388714. Ergothioneine Human Metabolome Database Ergothioneine KEGG Compound...

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Ligustilide

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range of components, including polysaccharides. "Ligustilide". Human Metabolome Database. Gijbels, M.J.M., Fischer, F.C., Scheffer, J.J.C.; et al. (1983)...

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Deoxyguanosine

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from the original on 2 January 2017. Retrieved 2 January 2017. "Human Metabolome Database (HMDB) metabocard for Deoxyguanosine (HMDB0000085)". v t e...

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Lipoamide

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and animal-based foods. Lipoic acid "Metabocard for Lipoamide". Human Metabolome Database. 14 September 2021. HMDB0000962. Retrieved 30 November 2022. J...

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Antileukotriene

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from asthmatic patients. "Enzymes". Hyperforin (HMDB0030463). Human Metabolome Database. 3.6. University of Alberta. 30 June 2013. Retrieved 12 December...

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Acrylamide

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 842. doi:10.1039/9781849733069-FP001. ISBN 978-0-85404-182-4. "Human Metabolome Database: Showing metabocard for Acrylamide (HMDB0004296)". Sigma-Aldrich...

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Octanol

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isomers of octanol,[citation needed] including: 1-Octanol 2-Octanol 2-Ethylhexanol C8H18O "Octanol". Human Metabolome Database. Retrieved 29 December 2019....

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Hydrogen cyanide

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Wiley-VCH. doi:10.1002/14356007.a08_159.pub2. ISBN 978-3527306732. "Human Metabolome Database: Showing metabocard for Hydrogen cyanide (HMDB0060292)". "Cyanide...

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Apache Lucene

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MojoMojo wiki. It is also used by the Human Metabolome Database (HMDB) and the Toxin and Toxin-Target Database (T3DB). MongoDB Atlas Search – a cloud-native...

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Adenosine monophosphate

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201506593. PMC 4678511. PMID 26435376. "Adenosine monophosphate". The Human Metabolome Database. Retrieved 3 July 2020. Baker, Julien S.; McCormick, Marie Clare;...

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Opioid peptide

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agonists (Human) [are] big dynorphin (PDYN, P01213), dynorphin A (PDYN, P01213) "Dynorphin A 1–8". HMDB Version 4.0. Human Metabolome Database. 27 September...

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ChemSpider

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ChemSpider Identifier. The database sources include: EPA DSSTox U.S. Food and Drug Administration (FDA) Human Metabolome Database Journal of Heterocyclic...

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Indole

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sporogenes. IPA metabolism diagram "3-Indolepropionic acid". Human Metabolome Database. University of Alberta. Retrieved 12 June 2018. Chyan YJ, Poeggeler...

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