1. HMDB 4.0: the human metabolome database for 2018
- Author
-
Allison Pon, Carin Li, Zinat Sayeeda, An Chi Guo, Craig Knox, Hasan Badran, David Arndt, Vanessa Neveu, Mark V. Berjanskii, Kevin Y. H. Liang, Yannick Djoumbou Feunang, Augustin Scalbert, Naama Karu, Claudine Manach, Rosa Vázquez-Fresno, Arnau Serra-Cayuela, Jason R. Grant, Ana Marcu, Sandeep Singhal, Yongjie Liang, Rupa Mandal, Nazanin Assempour, Yifeng Liu, David S. Wishart, Elvis J. Lo, Michael Wilson, Daniel Johnson, Tanvir Sajed, Department of Biological Sciences, The Open University [Milton Keynes] (OU), Department of Computer Science, Duke University [Durham], Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, International Agency for Cancer Research (IACR), OMx Personal Health Analytics, Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Genome Alberta (a division of Genome Canada), The Canadian Institutes of Health Research (CIHR), Western Economic Diversification (WED), Alberta Innovates Health Solutions (AIHS). Funding for open access charge: Genome Canada., Wishart, David S, Unité de Nutrition Humaine (UNH), and Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])
- Subjects
0301 basic medicine ,Databases, Factual ,Bioinformatics ,Metabolite ,Chimie analytique ,metabolite ,Disease Association ,Computational biology ,Biology ,01 natural sciences ,Gas Chromatography-Mass Spectrometry ,analyse métabolomique ,03 medical and health sciences ,chemistry.chemical_compound ,User-Computer Interface ,Metabolomics ,Tandem Mass Spectrometry ,[CHIM.ANAL]Chemical Sciences/Analytical chemistry ,Genetics ,Metabolome ,Database Issue ,Humans ,Human Metabolome Database ,Spectral data ,être humain ,Nuclear Magnetic Resonance, Biomolecular ,database ,Text searching ,010401 analytical chemistry ,Biological classification ,0104 chemical sciences ,3. Good health ,030104 developmental biology ,chemistry ,Bio-informatique ,[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] ,Analytical chemistry ,Databases, Chemical ,Metabolic Networks and Pathways - Abstract
The Human Metabolome Database or HMDB (www.hmdb.ca) is a web-enabled metabolomic database containing comprehensive information about human metabolites along with their biological roles, physiological concentrations, disease associations, chemical reactions, metabolic pathways, and reference spectra. First described in 2007, the HMDB is now considered the standard metabolomic resource for human metabolic studies. Over the past decade the HMDB has continued to grow and evolve in response to emerging needs for metabolomics researchers and continuing changes in web standards. This year's update, HMDB 4.0, represents the most significant upgrade to the database in its history. For instance, the number of fully annotated metabolites has increased by nearly threefold, the number of experimental spectra has grown by almost fourfold and the number of illustrated metabolic pathways has grown by a factor of almost 60. Significant improvements have also been made to the HMDB’s chemical taxonomy, chemical ontology, spectral viewing, and spectral/text searching tools. A great deal of brand new data has also been added to HMDB 4.0. This includes large quantities of predicted MS/MS and GC–MS reference spectral data as well as predicted (physiologically feasible) metabolite structures to facilitate novel metabolite identification. Additional information on metabolite-SNP interactions and the influence of drugs on metabolite levels (pharmacometabolomics) has also been added. Many other important improvements in the content, the interface, and the performance of the HMDB website have been made and these should greatly enhance its ease of use and its potential applications in nutrition, biochemistry, clinical chemistry, clinical genetics, medicine, and metabolomics science.
- Published
- 2018
- Full Text
- View/download PDF