Human Metabolome Database


The '''Human Metabolome Database chemical data, 2) clinical data, and 3) molecular biology/biochemistry data. The chemical data includes 41,514 metabolite structures with detailed descriptions along with nearly 10,000 NMR, GC-MS and LC/MS spectra.
The clinical data includes information on >10,000 metabolite-biofluid concentrations and metabolite concentration information on more than 600 different human diseases. The biochemical data includes 5,688 protein sequences and more than 5000 biochemical reactions that are linked to these metabolite entries. Each metabolite entry in the HMDB contains more than 110 data fields with 2/3 of the information being devoted to chemical/clinical data and the other 1/3 devoted to enzymatic or biochemical data. Many data fields are hyperlinked to other databases 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.
Four additional databases, DrugBank, T3DB, SMPDB and FooDB are also part of the HMDB suite of databases. DrugBank contains equivalent information on ~1600 drug and drug metabolites, T3DB contains information on 3100 common toxins and environmental pollutants, SMPDB contains pathway diagrams for 700 human metabolic and disease pathways, while FooDB contains equivalent information on ~28,000 food components and food additives.

Version history

The first version of HMDB was released on January 1, 2007, followed by two subsequent versions on January 1, 2009, August 1, 2009, September 18, 2012 and Jan. 1, 2013, 2017. Details for each of the major HMDB versions is provided in Table 1.
Database Feature or Content StatusHMDB HMDB HMDB HMDB
Number of metabolites21806408
Number of unique metabolite synonyms
Number of compounds with disease links8621002394822605
Number of compounds with biofluid or tissue concentration data88344136796
Number of compounds with chemical synthesis references2201647886372604
Number of compounds with experimental reference 1H and or 13C NMR spectra38579210542801
Number of compounds with reference MS/MS spectra39079912491544
Number of compounds with reference GC-MS reference data02798847418
Number of human-specific pathway maps2658442
Number of compounds in Human Metabolome Library6079201031
Number of HMDB data fields91102114130
'Number of predicted molecular properties''2210

Scope and access

All data in HMDB is non-proprietary or is derived from a non-proprietary source. It is freely accessible and available to anyone. In addition, nearly every data item is fully traceable and explicitly referenced to the original source. HMDB data is available through a public web interface and downloads.