HMDB 3.0--The Human Metabolome Database in 2013

Area of Science:

• Biochemistry
• Bioinformatics
• Systems Biology

Background:

• The Human Metabolome Database (HMDB) is a crucial resource for metabolomics research.
• Previous versions have supported numerous scientific studies since 2007.

Purpose of the Study:

• To detail the significant enhancements and expansions in the HMDB version 3.0 release.
• To highlight new data types, visualization tools, and search functionalities.

Main Methods:

• Expanded metabolite annotation to include 'detected' and 'expected' compounds.
• Increased the number of entries with concentration data, reference spectra, and detailed data fields.
• Developed enhanced database visualization tools, including spectral viewers, chemical substructure searches, and interactive pathway maps.

Main Results:

• The HMDB 3.0 release features over 40,000 metabolite entries, a 600% increase from version 2.0.
• Significant improvements in data quantity per entry, including biofluid/tissue concentrations and spectral data.
• Enhanced user interface with advanced search capabilities and interactive pathway visualizations.

Conclusions:

• HMDB 3.0 represents a substantial advancement in human metabolome data resources.
• The expanded content and improved tools will further facilitate research in metabolomics, clinical biochemistry, and systems biology.