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. 2018 Jan 4;46(D1):D608-D617.
doi: 10.1093/nar/gkx1089.

HMDB 4.0: The Human Metabolome Database for 2018

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Free PMC article

HMDB 4.0: The Human Metabolome Database for 2018

David S Wishart et al. Nucleic Acids Res. .
Free PMC article

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.

Figures

Figure 1.
Figure 1.
An illustration of how the lipid structures looked like in HMDB 3.0 (A) and how they now appear in HMDB 4.0 (B) for the compound Cardiolipin(16:0/16:1/16:1/22:6).
Figure 2.
Figure 2.
A schematic diagram of the ontology structure in HMDB 4.0 for the first three ontological levels.

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References

    1. Wishart D.S. Metabolomics: applications to food science and nutrition research. Trends Food Sci. Technol. 2008; 19:482–493.
    1. Wishart D.S. Current progress in computational metabolomics. Brief. Bioinf. 2007; 8:279–293. - PubMed
    1. Benson D.A., Cavanaugh M., Clark K., Karsch-Mizrachi I., Lipman D.J., Ostell J., Sayers E.W. GenBank. Nucleic Acids Res. 2017; 45:D37–D42. - PMC - PubMed
    1. The UniProt Consortium UniProt: the universal protein knowledgebase. Nucleic Acids Res. 2017; 45:D158–D169. - PMC - PubMed
    1. Kanehisa M., Furumichi M., Tanabe M., Sato Y., Morishima K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 2017; 45:D353–D361. - PMC - PubMed

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