HMDB 3.0—The Human Metabolome Database in 2013

Abstract

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.).

A Sensitive and Wide Coverage Ambient Mass Spectrometry Imaging Method for Functional Metabolites Based Molecular Histology

“…However, the fact that over 41 000 metabolites of different classes appear in the extremely complex organism with significant content variation has made its detection difficult 2. The core of the problem lies in developing an untargeted, high sensitive, wide coverage, and high chemical specific imaging method, visualizing the spatial distribution of numerous metabolites in their native state, especially for those with extensive biofunctions but low‐abundance in tissue.…”

Identification and Quantitative Assessment of Uremic Solutes as Inhibitors of Renal Organic Anion Transporters, OAT1 and OAT3

“…Collectively, our data suggests CL sec deteriorate more extensively than GFR. Renal clearance by secretion measured in off-dialysis period recovered in patients with CKD Stage 5d (Figure 5c) 67 Canavan disease is an autosomal recessive disease characterized by progressive loss of myelin in brain neuron cells. Patients with Canavan have plasma uric acid concentration as high as ∼1700 μM, which is 3-fold higher than the concentrations in CKD patients.…”

Pharmacometabolomic Assessments of Atenolol and Hydrochlorothiazide Treatment Reveal Novel Drug Response Phenotypes

“…Groups were defined by drug (ATEN or HCTZ), direction of metabolite association (increased or decreased), and race. In order to combine metabolite level to a pathway level score, a correlated Lancaster approach21 was performed using data from the Human Metabolome Database version 3.5,22 and International Union of Pure and Applied Chemistry International Chemical Identifier codes for annotation. This approach uses correlation information from permutation testing of all known metabolites in the study rather than using a list based on a metabolite significance threshold.…”