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Human Metabolome Database
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<h2 id="version-history">Version history</h2> <p>The first version of HMDB was released on January 1, 2007,<a class="footnote-ref" id="fnref:12" href="#fn:12"><sup>12</sup></a> followed by two subsequent versions on January 1, 2009 (version 2.0),<a class="footnote-ref" id="fnref:13" href="#fn:13"><sup>13</sup></a> August 1, 2009 (version 2.5), September 18, 2012 (version 3.0)<a class="footnote-ref" id="fnref:14" href="#fn:14"><sup>14</sup></a> and Jan. 1, 2013 (version 3.5),<a class="footnote-ref" id="fnref:15" href="#fn:15"><sup>15</sup></a> 2017 (version 4.0).<a class="footnote-ref" id="fnref:16" href="#fn:16"><sup>16</sup></a> 2022 (version 5.0).<a class="footnote-ref" id="fnref:17" href="#fn:17"><sup>17</sup></a> Details for each of the major HMDB versions (up to version 5.0) is provided in Table 1. </p> Table 1. Content comparison of HMDB versions<table><tbody><tr><th>Database Feature or Content Status</th><th>HMDB (v1.0)</th><th>HMDB (v2.0)</th><th>HMDB (v3.0)</th><th>HMDB (v4.0)</th><th>HMDB (v5.0)</th></tr><tr><td><i>Number of metabolites</i></td><td>2,180</td><td>6,408</td><td>37,170</td><td>114,100</td><td>220,945</td></tr><tr><td><i>Number of unique metabolite synonyms</i></td><td>27,700</td><td>43,882</td><td>152,364</td><td>−</td><td>−</td></tr><tr><td><i>Number of compounds with disease links</i></td><td>862</td><td>1,002</td><td>3,948</td><td>22,605</td><td>22,600</td></tr><tr><td><i>Number of compounds with biofluid or tissue concentration data</i></td><td>883</td><td>4,413</td><td>6,796</td><td>−</td><td>−</td></tr><tr><td><i>Number of compounds with chemical synthesis references</i></td><td>220</td><td>1,647</td><td>8,863</td><td>72,604</td><td>78,841</td></tr><tr><td><i>Number of compounds with experimental reference 1H and or 13C NMR spectra</i></td><td>385</td><td>792</td><td>1,054</td><td>2,801</td><td>12,216</td></tr><tr><td><i>Number of compounds with reference MS/MS spectra</i></td><td>390</td><td>799</td><td>1,249</td><td>1,544</td><td>4,064</td></tr><tr><td><i>Number of compounds with reference GC-MS reference data</i></td><td>0</td><td>279</td><td>884</td><td>7,418</td><td>11,493</td></tr><tr><td><i>Number of human-specific pathway maps</i></td><td>26</td><td>58</td><td>442</td><td>−</td><td>−</td></tr><tr><td><i>Number of compounds in Human Metabolome Library</i></td><td>607</td><td>920</td><td>1,031</td><td>−</td><td>−</td></tr><tr><td><i>Number of HMDB data fields</i></td><td>91</td><td>102</td><td>114</td><td>130</td><td>130</td></tr><tr><td><i>Number of predicted molecular properties</i></td><td>2</td><td>2</td><td>10</td><td>−</td><td>−</td></tr></tbody></table> <h2 id="scope-and-access">Scope and access</h2> <p>All 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. </p> <h2 id="see-also">See also</h2> <ul><li><a href="/facts/KEGG/pK5La8ad">KEGG</a></li> <li><a href="/facts/DrugBank/ycxhRlLA">DrugBank</a></li> <li><a href="/facts/SMPDB/aSSX0I25">SMPDB</a></li> <li><a href="/facts/MetaCyc/46YHwHqq">MetaCyc</a></li> <li><a href="/facts/Bovine_Metabolome_Database/Bx8Qmguc">Bovine Metabolome Database</a></li> <li><a href="/facts/Metabolome/uY3lFQ9h">Metabolome</a></li> <li><a href="/facts/Metabolomics/9WytJVN7">Metabolomics</a></li> <li><a href="/facts/List_of_biological_databases/z1o0kcKt">List of biological databases</a></li></ul> <h2 id="references">References</h2> <ol> <li id="fn:1"><p>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 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899095" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899095</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li> <li id="fn:2"><p>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. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686599" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686599</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li> <li id="fn:3"><p>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 href="978-0471250951" target="_blank">978-0471250951</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li> <li id="fn:4"><p>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 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531200" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531200</a> <a href="#fnref:4" class="footnote-back-ref">↩</a></p></li> <li id="fn:5"><p>"Human Metabolome Project". Retrieved 13 February 2013. <a href="http://metabolomics.ca/" target="_blank">http://metabolomics.ca/</a> <a href="#fnref:5" class="footnote-back-ref">↩</a></p></li> <li id="fn:6"><p>"Human Metabolome Project". Retrieved 13 February 2013. <a href="http://metabolomics.ca/" target="_blank">http://metabolomics.ca/</a> <a href="#fnref:6" class="footnote-back-ref">↩</a></p></li> <li id="fn:7"><p>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. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347430" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347430</a> <a href="#fnref:7" class="footnote-back-ref">↩</a></p></li> <li id="fn:8"><p>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. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238889" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238889</a> <a href="#fnref:8" class="footnote-back-ref">↩</a></p></li> <li id="fn:9"><p>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. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013709" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013709</a> <a href="#fnref:9" class="footnote-back-ref">↩</a></p></li> <li id="fn:10"><p>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. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808899" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808899</a> <a href="#fnref:10" class="footnote-back-ref">↩</a></p></li> <li id="fn:11"><p>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 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808928" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808928</a> <a href="#fnref:11" class="footnote-back-ref">↩</a></p></li> <li id="fn:12"><p>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 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899095" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899095</a> <a href="#fnref:12" class="footnote-back-ref">↩</a></p></li> <li id="fn:13"><p>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. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686599" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686599</a> <a href="#fnref:13" class="footnote-back-ref">↩</a></p></li> <li id="fn:14"><p>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 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531200" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531200</a> <a href="#fnref:14" class="footnote-back-ref">↩</a></p></li> <li id="fn:15"><p>"Human Metabolome Database Release Notes". <a href="http://www.hmdb.ca/release-notes" target="_blank">http://www.hmdb.ca/release-notes</a> <a href="#fnref:15" class="footnote-back-ref">↩</a></p></li> <li id="fn:16"><p>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. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753273" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753273</a> <a href="#fnref:16" class="footnote-back-ref">↩</a></p></li> <li id="fn:17"><p>"Human Metabolome Database Release Notes". <a href="http://www.hmdb.ca/release-notes" target="_blank">http://www.hmdb.ca/release-notes</a> <a href="#fnref:17" class="footnote-back-ref">↩</a></p></li> </ol>