The Human Metabolome Database (HMDB) is a comprehensive, high-quality, freely accessible, online database of

small molecule In molecular biology and pharmacology, a small molecule or micromolecule is a low molecular weight (≤ 1000 daltons) organic compound that may regulate a biological process, with a size on the order of 1 nm. Many drugs are small molecules; ...

metabolites In biochemistry, a metabolite is an intermediate or end product of metabolism. The term is usually used for small molecules. Metabolites have various functions, including fuel, structure, signaling, stimulatory and inhibitory effects on enzymes, c ...

found in the human body. It has been created by the Human Metabolome Project funded by Genome Canada and is one of the first dedicated

metabolomics Metabolomics is the scientific study of chemical processes involving metabolites, the small molecule substrates, intermediates, and products of cell metabolism. Specifically, metabolomics is the "systematic study of the unique chemical fingerpri ...

databases. The HMDB facilitates human metabolomics research, including the identification and characterization of human metabolites using

NMR spectroscopy Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy or magnetic resonance spectroscopy (MRS), is a spectroscopic technique based on re-orientation of atomic nuclei with non-zero nuclear spins in an external magnetic f ...

, 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 Molecular biology is a branch of biology that seeks to understand the molecule, molecular basis of biological activity in and between Cell (biology), cells, including biomolecule, biomolecular synthesis, modification, mechanisms, and interactio ...

biochemistry Biochemistry, or biological chemistry, is the study of chemical processes within and relating to living organisms. A sub-discipline of both chemistry and biology, biochemistry may be divided into three fields: structural biology, enzymology, a ...

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 A disease is a particular abnormal condition that adversely affects the structure or function of all or part of an organism and is not immediately due to any external injury. Diseases are often known to be medical conditions that are asso ...

. The biochemical data includes 5,688

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...

(and

DNA Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...

) sequences and more than 5,000 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 (

KEGG KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances. KEGG is utilized for bioinformatics research and education, including data analysis ...

, MetaCyc,

PubChem PubChem is a database of Chemistry, chemical molecules and their activities against biological assays. The system is maintained by the National Center for Biotechnology Information (NCBI), a component of the National Library of Medicine, which ...

Protein Data Bank The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules such as proteins and nucleic acids, which is overseen by the Worldwide Protein Data Bank (wwPDB). This structural data is obtained a ...

, ChEBI,

Swiss-Prot UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from ...

, and

GenBank The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. It is produced and maintained by the National Center for Biotechnology Information (NCBI; a par ...

) and a variety of structure and pathway viewing applets. The HMDB database supports extensive text, sequence, spectral,

chemical structure A chemical structure of a molecule is a spatial arrangement of its atoms and their chemical bonds. Its determination includes a chemist's specifying the molecular geometry and, when feasible and necessary, the electronic structure of the target m ...

and relational query searches. It has been widely used in metabolomics, clinical chemistry,

biomarker In biomedical contexts, a biomarker, or biological marker, is a measurable indicator of some biological state or condition. Biomarkers are often measured and evaluated using blood, urine, or soft tissues to examine normal biological processes, ...

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 ~1,600 drug and drug metabolites, T3DB contains information on 3,100 common

toxin A toxin is a naturally occurring poison produced by metabolic activities of living cells or organisms. They occur especially as proteins, often conjugated. The term was first used by organic chemist Ludwig Brieger (1849–1919), derived ...

s and environmental

pollutant A pollutant or novel entity is a substance or energy introduced into the environment that has undesired effect, or adversely affects the usefulness of a resource. These can be both naturally forming (i.e. minerals or extracted compounds like oi ...

s, SMPDB contains pathway diagrams for 700 human metabolic and disease pathways, while FooDB contains equivalent information on ~28,000 food components and

food additive Food additives are substances added to food to preserve flavor or enhance taste, appearance, or other sensory qualities. Some additives, such as vinegar ( pickling), salt ( salting), smoke ( smoking) and sugar ( crystallization), have been used f ...

Version history

The first version of HMDB was released on January 1, 2007, followed by two subsequent versions on January 1, 2009 (version 2.0), August 1, 2009 (version 2.5), September 18, 2012 (version 3.0) and Jan. 1, 2013 (version 3.5), 2017 (version 4.0). 2022 (version 5.0). Details for each of the major HMDB versions (up to version 5.0) is provided in Table 1.

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.

References

{{Genomics Biochemistry databases Metabolomic databases Medical databases Food databases Human metabolites

Version history

Scope and access

See also

References