Human Metabolome Database

The Human Metabolome Database

[1][2][3][4] Human Metabolome Database
(HMDB) is a comprehensive, high-quality,
freely accessible, online database of small molecule
metabolites found in the human body. It bas 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
Content
the identification and characterization of human
metabolites using NMR spectroscopy, GC-MS Description Metabolomics database
spectrometry and LC/MS spectrometry. To aid in Data types Human metabolite structures,
this discovery process, the HMDB contains three captured metabolite descriptions,
kinds of data: 1) chemical data, 2) clinical data, and metabolite reactions,
3) molecular biology/biochemistry data (Fig. 1–3).
metabolite enzymes and
The chemical data includes 41,514 metabolite
transporters, human enzyme
structures with detailed descriptions along with
and transporter sequences,
nearly 10,000 NMR, GC-MS and LC/MS spectra.
human metabolic pathways,
The clinical data includes information on >10,000 normal and abnormal
metabolite-biofluid concentrations and metabolite metabolite concentrations in
concentration information on more than 600 humans, associated diseases,
different human diseases. The biochemical data chemical properties,
includes 5,688 protein (and DNA) sequences and nomenclature, synonyms,
more than 5,000 biochemical reactions that are
chemical taxonomy, metabolite
linked to these metabolite entries.[5] Each metabolite
NMR spectra, metabolite GC-
entry in the HMDB contains more than 110 data
MS spectra, metabolite LC-MS
fields with 2/3 of the information being devoted to
chemical/clinical data and the other 1/3 devoted to spectra
enzymatic or biochemical data. Many data fields are Contact
hyperlinked to other databases (KEGG, MetaCyc,
Research center University of Alberta and The
PubChem, Protein Data Bank, ChEBI, Swiss-Prot,
Metabolomics Innovation
and GenBank) and a variety of structure and
pathway viewing applets. The HMDB database Centre
supports extensive text, sequence, spectral, chemical Laboratory David S. Wishart
structure and relational query searches. It has been Primary citation HMDB: the Human
widely used in metabolomics, clinical chemistry,
Metabolome Database.[1]
biomarker discovery and general biochemistry
education. Access
Website http://www.hmdb.ca
Four additional databases, DrugBank,[6][7][8]
Download URL http://www.hmdb.ca/downloads
T3DB,[9] SMPDB [10] and FooDB are also part of
the HMDB suite of databases. DrugBank contains Miscellaneous
equivalent information on ~1,600 drug and drug Data release Every 2 years with monthly
metabolites, T3DB contains information on 3,100 frequency corrections and updates
common toxins and environmental pollutants,
Curation policy Manually curated
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,[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

HMDB HMDB HMDB HMDB HMDB
Database Feature or Content Status
(v1.0) (v2.0) (v3.0) (v4.0) (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

883 4,413 6,796 − −
concentration data

Number of compounds with chemical synthesis

220 1,647 8,863 72,604 78,841
references
Number of compounds with experimental
385 792 1,054 2,801 12,216
reference 1H and or 13C NMR spectra

Number of compounds with reference MS/MS

390 799 1,249 1,544 4,064
spectra

Number of compounds with reference GC-MS

0 279 884 7,418 11,493
reference data
Number of human-specific pathway maps 26 58 442 − −

Number of compounds in Human Metabolome

607 920 1,031 − −
Library

Number of HMDB data fields 91 102 114 130 130

'Number of predicted molecular properties 2 2 10 − −

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.

See also
KEGG
DrugBank
SMPDB
MetaCyc
Bovine Metabolome Database
 Metabolome
Metabolomics
List of biological databases

References
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Lewis, Mike; Coutouly, Marie-Aude; Forsythe, Ian J.; Tang, Peter; Shrivastava, Savita;
Jeroncic, Kevin; Stothard, Paul; Amegbey, Godwin; Block, David; Hau, David D.; Wagner,
James; Miniaci, Jessica; Clements, Melisa; Gebremedhin, Mulu; Guo, Natalie; Zhang, Ying;
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