HMDB

The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. It is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education. The database is designed to contain or link three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular biology/biochemistry data. The database contains 114,015 metabolite entries including both water-soluble and lipid soluble metabolites as well as metabolites that would be regarded as either abundant (> 1 uM) or relatively rare (< 1 nM). Additionally, 5,702 protein sequences are linked to these metabolite entries. Each MetaboCard entry contains 130 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, PubChem, MetaCyc, ChEBI, PDB, UniProt, and GenBank) and a variety of structure and pathway viewing applets. The HMDB database supports extensive text, sequence, chemical structure and relational query searches. Four additional databases, DrugBank, T3DB, SMPDB and FooDB are also part of the HMDB suite of databases. DrugBank contains equivalent information on  2280 drug and drug metabolites, T3DB contains information on  3670 common toxins and environmental pollutants, SMPDB contains pathway diagrams for  25,000 human metabolic and disease pathways, while FooDB contains equivalent information on  28,000 food components and food additives.


References in zbMATH (referenced in 9 articles )

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  1. Fertin, Guillaume; Fradin, Julien; Jean, Géraldine: The \textscMaximumColorful Arborescence problem: how (computationally) hard can it be? (2021)
  2. Ye, Lifeng; Beskos, Alexandros; De Iorio, Maria; Hao, Jie: Monte Carlo co-ordinate ascent variational inference (2020)
  3. Jalal K. Siddiqui, Elizabeth Baskin, Mingrui Liu, Carmen Z. Cantemir-Stone, Bofei Zhang, Russell Bonneville, Joseph P. McElroy, Kevin R. Coombes, Ewy A. Mathé: IntLIM: Integration using Linear Models of metabolomics and gene expression data (2018) arXiv
  4. Lachmann, Alexander; Ma’ayan, Avi: Lists2networks: integrated analysis of gene/protein lists (2010) ioport
  5. Van Iersel, Martijn P.; Pico, Alexander R.; Kelder, Thomas; Gao, Jianjiong; Ho, Isaac; Hanspers, Kristina; Conklin, Bruce R.; Evelo, Chris T. A.: The bridgedb framework: standardized access to gene, protein and metabolite identifier mapping services (2010) ioport
  6. Draper, John; Enot, David P.; Parker, David; Beckmann, Manfred; Snowdon, Stuart; Lin, Wanchang; Zubair, Hassan: Metabolite signal identification in accurate mass metabolomics data with mzeddb, an interactive \textitm/zannotation tool utilising predicted ionisation behaviour ’rules’ (2009) ioport
  7. Khanna, Varun; Ranganathan, Shoba: Physicochemical property space distribution among human metabolites, drugs and toxins (2009) ioport
  8. Wishart, David S.; Knox, Craig; Guo, Anchi; 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, Russell; Nazyrova, Alsu; Shaykhutdinov, Rustem; Li, Liang; Vogel, Hans J.; Forsythe, Ian J.: HMDB: a knowledgebase for the human metabolome (2009) ioport
  9. Wishart, David S.; Tzur, Dan; Knox, Craig; Eisner, Roman; Guo, Anchi; 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, Russell; Li, Liang; Marrie, Tom; Sykes, Brian D.; Vogel, Hans J.; Querengesser, Lori: HMDB: The human metabolome database. (2007) ioport