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HMDB 3.0—The Human Metabolome Database in 2013
The Human Metabolome Database (HMDB) (www.hmdb.ca) is a resource dedicated to providing scientists with the most current and comprehensive coverage of the human metabolome. Since its first release in 2007, the HMDB has been used to facilitate research for nearly 1000 published studies in metabolomic...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531200/ https://www.ncbi.nlm.nih.gov/pubmed/23161693 http://dx.doi.org/10.1093/nar/gks1065 |
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author | Wishart, David S. Jewison, Timothy Guo, An Chi Wilson, Michael Knox, Craig Liu, Yifeng Djoumbou, Yannick Mandal, Rupasri Aziat, Farid Dong, Edison Bouatra, Souhaila Sinelnikov, Igor Arndt, David Xia, Jianguo Liu, Philip Yallou, Faizath Bjorndahl, Trent Perez-Pineiro, Rolando Eisner, Roman Allen, Felicity Neveu, Vanessa Greiner, Russ Scalbert, Augustin |
author_facet | Wishart, David S. Jewison, Timothy Guo, An Chi Wilson, Michael Knox, Craig Liu, Yifeng Djoumbou, Yannick Mandal, Rupasri Aziat, Farid Dong, Edison Bouatra, Souhaila Sinelnikov, Igor Arndt, David Xia, Jianguo Liu, Philip Yallou, Faizath Bjorndahl, Trent Perez-Pineiro, Rolando Eisner, Roman Allen, Felicity Neveu, Vanessa Greiner, Russ Scalbert, Augustin |
author_sort | Wishart, David S. |
collection | PubMed |
description | The Human Metabolome Database (HMDB) (www.hmdb.ca) is a resource dedicated to providing scientists with the most current and comprehensive coverage of the human metabolome. Since its first release in 2007, the HMDB has been used to facilitate research for nearly 1000 published studies in metabolomics, clinical biochemistry and systems biology. The most recent release of HMDB (version 3.0) has been significantly expanded and enhanced over the 2009 release (version 2.0). In particular, the number of annotated metabolite entries has grown from 6500 to more than 40 000 (a 600% increase). This enormous expansion is a result of the inclusion of both ‘detected’ metabolites (those with measured concentrations or experimental confirmation of their existence) and ‘expected’ metabolites (those for which biochemical pathways are known or human intake/exposure is frequent but the compound has yet to be detected in the body). The latest release also has greatly increased the number of metabolites with biofluid or tissue concentration data, the number of compounds with reference spectra and the number of data fields per entry. In addition to this expansion in data quantity, new database visualization tools and new data content have been added or enhanced. These include better spectral viewing tools, more powerful chemical substructure searches, an improved chemical taxonomy and better, more interactive pathway maps. This article describes these enhancements to the HMDB, which was previously featured in the 2009 NAR Database Issue. (Note to referees, HMDB 3.0 will go live on 18 September 2012.). |
format | Online Article Text |
id | pubmed-3531200 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-35312002013-03-07 HMDB 3.0—The Human Metabolome Database in 2013 Wishart, David S. Jewison, Timothy Guo, An Chi Wilson, Michael Knox, Craig Liu, Yifeng Djoumbou, Yannick Mandal, Rupasri Aziat, Farid Dong, Edison Bouatra, Souhaila Sinelnikov, Igor Arndt, David Xia, Jianguo Liu, Philip Yallou, Faizath Bjorndahl, Trent Perez-Pineiro, Rolando Eisner, Roman Allen, Felicity Neveu, Vanessa Greiner, Russ Scalbert, Augustin Nucleic Acids Res Articles The Human Metabolome Database (HMDB) (www.hmdb.ca) is a resource dedicated to providing scientists with the most current and comprehensive coverage of the human metabolome. Since its first release in 2007, the HMDB has been used to facilitate research for nearly 1000 published studies in metabolomics, clinical biochemistry and systems biology. The most recent release of HMDB (version 3.0) has been significantly expanded and enhanced over the 2009 release (version 2.0). In particular, the number of annotated metabolite entries has grown from 6500 to more than 40 000 (a 600% increase). This enormous expansion is a result of the inclusion of both ‘detected’ metabolites (those with measured concentrations or experimental confirmation of their existence) and ‘expected’ metabolites (those for which biochemical pathways are known or human intake/exposure is frequent but the compound has yet to be detected in the body). The latest release also has greatly increased the number of metabolites with biofluid or tissue concentration data, the number of compounds with reference spectra and the number of data fields per entry. In addition to this expansion in data quantity, new database visualization tools and new data content have been added or enhanced. These include better spectral viewing tools, more powerful chemical substructure searches, an improved chemical taxonomy and better, more interactive pathway maps. This article describes these enhancements to the HMDB, which was previously featured in the 2009 NAR Database Issue. (Note to referees, HMDB 3.0 will go live on 18 September 2012.). Oxford University Press 2013-01 2012-11-17 /pmc/articles/PMC3531200/ /pubmed/23161693 http://dx.doi.org/10.1093/nar/gks1065 Text en © The Author(s) 2012. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com. |
spellingShingle | Articles Wishart, David S. Jewison, Timothy Guo, An Chi Wilson, Michael Knox, Craig Liu, Yifeng Djoumbou, Yannick Mandal, Rupasri Aziat, Farid Dong, Edison Bouatra, Souhaila Sinelnikov, Igor Arndt, David Xia, Jianguo Liu, Philip Yallou, Faizath Bjorndahl, Trent Perez-Pineiro, Rolando Eisner, Roman Allen, Felicity Neveu, Vanessa Greiner, Russ Scalbert, Augustin HMDB 3.0—The Human Metabolome Database in 2013 |
title | HMDB 3.0—The Human Metabolome Database in 2013 |
title_full | HMDB 3.0—The Human Metabolome Database in 2013 |
title_fullStr | HMDB 3.0—The Human Metabolome Database in 2013 |
title_full_unstemmed | HMDB 3.0—The Human Metabolome Database in 2013 |
title_short | HMDB 3.0—The Human Metabolome Database in 2013 |
title_sort | hmdb 3.0—the human metabolome database in 2013 |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531200/ https://www.ncbi.nlm.nih.gov/pubmed/23161693 http://dx.doi.org/10.1093/nar/gks1065 |
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