The chemical data includes 41,514 metabolite structures with detailed descriptions along with nearly 10,000 NMR, GC-MS and LC/MS spectra.

Many data fields are hyperlinked to other databases (KEGG, MetaCyc, PubChem, Protein Data Bank, ChEBI, Swiss-Prot, and GenBank) and a variety of structure and pathway viewing applets.

The HMDB database supports extensive text, sequence, spectral, chemical structure and relational query searches.

It has been widely used in metabolomics, clinical chemistry, biomarker discovery and general biochemistry education.

In addition, nearly every data item is fully traceable and explicitly referenced to the original source.