This article is about the Human Metabolome Database (HMDB.ca). For the Historical Marker Database (HMdb.org), see Historical Marker Database.
Human Metabolome Database
Content
Description
Metabolomics database
Data types captured
Human metabolite structures, metabolite descriptions, metabolite reactions, metabolite enzymes and transporters, human enzyme and transporter sequences, human metabolic pathways, normal and abnormal metabolite concentrations in humans, associated diseases, chemical properties, nomenclature, synonyms, chemical taxonomy, metabolite NMR spectra, metabolite GC-MS spectra, metabolite LC-MS spectra
Every 2 years with monthly corrections and updates
Curation policy
Manually curated
The Human Metabolome Database (HMDB)[1][2][3][4] is a comprehensive, high-quality, freely accessible, online database of small moleculemetabolites found in the human body. It has been created by the Human Metabolome Project funded by Genome Canada[5] and is one of the first dedicated metabolomics databases. The HMDB facilitates human metabolomics research, including the identification and characterization of human metabolites using NMR spectroscopy, GC-MS spectrometry and LC/MS spectrometry. To aid in this discovery process, the HMDB contains three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular biology/biochemistry data (Fig. 1–3). 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 (and DNA) sequences and more than 5,000 biochemical reactions that are linked to these metabolite entries.[5] 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 (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.
Four additional databases, DrugBank,[6][7][8] T3DB,[9] SMPDB [10] and FooDB are also part of the HMDB suite of databases. DrugBank contains equivalent information on ~1,600 drug and drug metabolites, T3DB contains information on 3,100 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.
The first version of HMDB was released on January 1, 2007,[1] followed by two subsequent versions on January 1, 2009 (version 2.0),[2] August 1, 2009 (version 2.5), September 18, 2012 (version 3.0)[4] and Jan. 1, 2013 (version 3.5),[11] 2017 (version 4.0).[12], 2022 (version 5.0).[11] Details for each of the major HMDB versions (up to version 5.0) is provided in Table 1.
Table 1. Content comparison of HMDB versions
Database Feature or Content Status
HMDB (v1.0)
HMDB (v2.0)
HMDB (v3.0)
HMDB (v4.0)
HMDB (v5.0)
Number of metabolites
2,180
6,408
37,170
114,100
220,945
Number of unique metabolite synonyms
27,700
43,882
152,364
−
−
Number of compounds with disease links
862
1,002
3,948
22,605
22,600
Number of compounds with biofluid or tissue concentration data
883
4,413
6,796
−
−
Number of compounds with chemical synthesis references
220
1,647
8,863
72,604
78,841
Number of compounds with experimental reference 1H and or 13C NMR spectra
385
792
1,054
2,801
12,216
Number of compounds with reference MS/MS spectra
390
799
1,249
1,544
4,064
Number of compounds with reference GC-MS reference data
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.
