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HMDB

HMDB

A database dontaining information about small molecule metabolites in human. Tools for text, sequence, chemcal structure searches.

Topic

Metabolomics, Small molecules, Surgery, NR, Modl organisms

Details

  • Operation: Database search, Deposition, Structure database search, Structural similarity search, Query and retrieval
  • Software interface: Web user interface
  • Language: Java, Perl
  • License: Not stated
  • Cost: Free
  • Version name: 4.0
  • Credit: Wishart DS, Tzur D, Knox C, Eisner R, Guo AC, Young N, Cheng D, Jewell K, Arndt D, Sawhney S, Fung C, Nikolai L, Lewis M, Coutouly MA, Forsythe I, Tang P, Shrivastava S, Jeroncic K, Stothard P, Amegbey G, Block D, Hau DD, Wagner J, Miniaci J, Clements M, Gebremedhin M, Guo N, Zhang Y, Duggan GE, Macinnis GD, Weljie AM, Dowlatabadi R, Bamforth F, Clive D, Greiner R, Li L, Marrie T, Sykes BD, Vogel HJ, Querengesser L.
  • Contact: http://www.hmdb.ca/w/contact
  • Collection: -

Publications

Wishart DS, Tzur D, Knox C, Eisner R, Guo AC, Young N, Cheng D, Jewell K, Arndt D, Sawhney S, Fung C, Nikolai L, Lewis M, Coutouly MA, Forsythe I, Tang P, Shrivastava S, Jeroncic K, Stothard P, Amegbey G, Block D, Hau DD, Wagner J, Miniaci J, Clements M, Gebremedhin M, Guo N, Zhang Y, Duggan GE, Macinnis GD, Weljie AM, Dowlatabadi R, Bamforth F, Clive D, Greiner R, Li L, Marrie T, Sykes BD, Vogel HJ, Querengesser L "HMDB: the Human Metabolome Database." Nucleic Acids Res. 2007; 35(Database issue):D521-6 https://doi.org/10.1093/nar/gkl923
PMID: 17202168
PMCID: PMC1899095


Wishart DS, Knox C, Guo AC, Eisner R, Young N, Gautam B, Hau DD, Psychogios N, Dong E, Bouatra S, Mandal R, Sinelnikov I, Xia J, Jia L, Cruz JA, Lim E, Sobsey CA, Shrivastava S, Huang P, Liu P, Fang L, Peng J, Fradette R, Cheng D, Tzur D, Clements M, Lewis A, De Souza A, Zuniga A, Dawe M, Xiong Y, Clive D, Greiner R, Nazyrova A, Shaykhutdinov R, Li L, Vogel HJ, Forsythe I "HMDB: a knowledgebase for the human metabolome." Nucleic Acids Res. 2009; 37(Database issue):D603-10 https://doi.org/10.1093/nar/gkn810
PMID: 18953024
PMCID: PMC2686599


Wishart DS, Jewison T, Guo AC, Wilson M, Knox C, Liu Y, Djoumbou Y, Mandal R, Aziat F, Dong E, Bouatra S, Sinelnikov I, Arndt D, Xia J, Liu P, Yallou F, Bjorndahl T, Perez-Pineiro R, Eisner R, Allen F, Neveu V, Greiner R, Scalbert A "HMDB 3.0--The Human Metabolome Database in 2013." Nucleic Acids Res. 2013; 41(Database issue):D801-7 https://doi.org/10.1093/nar/gks1065
PMID: 23161693
PMCID: PMC3531200


Wishart DS, Feunang YD, Marcu A, Guo AC, Liang K, Vázquez-Fresno R, Sajed T, Johnson D, Li C, Karu N, Sayeeda Z, Lo E, Assempour N, Berjanskii M, Singhal S, Arndt D, Liang Y, Badran H, Grant J, Serra-Cayuela A, Liu Y, Mandal R, Neveu V, Pon A, Knox C, Wilson M, Manach C, Scalbert A "HMDB 4.0: the human metabolome database for 2018." Nucleic Acids Res. 2018; 46(D1):D608-D617 https://doi.org/10.1093/nar/gkx1089
PMID: 29140435
PMCID: PMC5753273


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