The Nutritional Metabolomics Database is a global open-source library of small molecules for use in human nutrition metabolomics, as part of the NuGO Metabolomics Initiative.
HMDB – Version 2.0 has just been released! The latest release of the HMDB now has detailed information on 6534 experimentally confirmed metabolites, representing an expansion of nearly 300% over version 1.0. Currently about 60% of the metabolites in the HMDB have been identified or confirmed by the HMDB's team of analytical chemists using NMR, LC-MS or GC-MS methods applied to a variety of human biofluids. Likewise, approximately 45% of the metabolites in the HMDB have been identified and archived through literature surveys or electronic data mining.
In addition to substantially increasing the number of metabolite entries we have also increased the completeness of the HMDB's annotations for hundreds of metabolites by adding many more detailed compound descriptions, including more synonyms (10% increase), doubling the number of compounds with NMR and MS spectra, tripling the number of compounds with biofluid concentration data and increasing the number of compounds with synthesis records by a factor of six.
Thanks to the feedback provided by HMDB's user community, a number of new data fields have been added to each MetaboCard in order to facilitate certain types of queries or comparisons. These include Chemical Source information (endogenous vs. exogenous), Physiological Charge, Experimental and Predicted logP, HMDB Pathway Images, General Metabolite References and Macromolecular Interacting Partners. New data fields have also been added for the BiGG database, Wikipedia and METLIN while extra data fields for GeneCard IDs, GeneAtlas IDs and HGNC IDs have been added for each of the corresponding enzymes. In addition to these changes, new data fields for NMR assignment files (both 1H and 13C) in the BMRB NMR* exchange format have been inserted as well as data fields for experimental 1H-13C HSQC Spectra, Simplified TOCSY Spectra and BMRB TOCSY Spectra.
We believe that one of the more important improvements to the HMDB concerns the addition of nearly 60 hand-drawn, zoomable, fully hyperlinked human metabolic pathway maps. Unlike most on-line metabolic maps, these HMDB pathway maps are quite specific to human metabolism and explicitly show the subcellular compartments where specific reactions are known to take place. All chemical structures in these pathway maps are hyperlinked to HMDB MetaboCards and all enzymes are hyperlinked to UniProt data cards for human enzymes.