This article is about the Human Metabolome Database (HMDB.ca). For the Historical Marker Database (HMdb.org), see Historical Marker Database.
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
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 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.
^ abWishart, 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.
^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.
The HumanMetabolomeDatabase (HMDB) is a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in the human...
biofluid-specific metabolomedatabases. Some of the better known metabolomedatabases include the HumanMetabolomeDatabase or HMDB, the Yeast MetabolomeDatabase or...
The Golm MetabolomeDatabase (GMD) is a gas chromatography (GC) – mass spectrometry (MS) reference library dedicated to metabolite profiling experiments...
Serum Metabolomedatabase is a free web database about small molecule metabolites found in human serum and their concentration values. The database includes...
doi:10.1021/ed100545v. "HumanMetabolomeDatabase: Showing metabocard for Allura red AC (HMDB0032884)". HumanMetabolomeDatabase. 11 September 2012. Retrieved...
suite of metabolomics databases that also includes HumanMetabolomeDatabase, DrugBank, and the Toxin and Toxin-Target Database (T3DB). While DrugBank...
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 HumanMetabolomeDatabase...
Retrieved 18 July 2015. "Pyrroloquinoline quinone (HMDB13636)". HumanMetabolomeDatabase. University of Alberta. Retrieved 19 July 2015, citing: PMID 2558842:...
pp. 5–94 to 5–98. ISBN 978-1439855119. "Chlorocarbonic acid". HumanMetabolomeDatabase. Smith, Brian. "The C=O Bond, Part VIII: Review". Spectroscopy...
range of components, including polysaccharides. "Ligustilide". HumanMetabolomeDatabase. Gijbels, M.J.M., Fischer, F.C., Scheffer, J.J.C.; et al. (1983)...
and animal-based foods. Lipoic acid "Metabocard for Lipoamide". HumanMetabolomeDatabase. 14 September 2021. HMDB0000962. Retrieved 30 November 2022. J...
from asthmatic patients. "Enzymes". Hyperforin (HMDB0030463). HumanMetabolomeDatabase. 3.6. University of Alberta. 30 June 2013. Retrieved 12 December...
MojoMojo wiki. It is also used by the HumanMetabolomeDatabase (HMDB) and the Toxin and Toxin-Target Database (T3DB). MongoDB Atlas Search – a cloud-native...
agonists (Human) [are] big dynorphin (PDYN, P01213), dynorphin A (PDYN, P01213) "Dynorphin A 1–8". HMDB Version 4.0. HumanMetabolomeDatabase. 27 September...
ChemSpider Identifier. The database sources include: EPA DSSTox U.S. Food and Drug Administration (FDA) HumanMetabolomeDatabase Journal of Heterocyclic...