Human Metabolome Database

{{Short description|Database of human metabolites}}

{{about|the Human Metabolome Database (HMDB.ca)|the Historical Marker Database (HMdb.org)|Historical Marker Database}}

{{Infobox biodatabase

|title = Human Metabolome Database

|logo = 150px

|description = Metabolomics database

|scope = 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

|center = University of Alberta and The Metabolomics Innovation Centre

|laboratory = David S. Wishart

|author =

|citation = HMDB: the Human Metabolome Database.{{cite HMDB|1.0}}

|released =

|format =

|url = http://www.hmdb.ca

|download = http://www.hmdb.ca/downloads

|frequency = Every 2 years with monthly corrections and updates

|curation = Manually curated

}}

The Human Metabolome Database (HMDB){{cite HMDB|2.0}}{{cite journal |last1=Forsythe |first1=Ian J. |author2-link=David S. Wishart |last2=Wishart |first2=David S. |title=Exploring Human Metabolites Using the Human Metabolome Database |journal=Current Protocols in Bioinformatics |date=March 1, 2009 |volume=25 |pages=14.8.1–14.8.45 |pmid=19274632 |doi=10.1002/0471250953.bi1408s25 |isbn=978-0471250951|s2cid=24291704 }}{{cite HMDB|3.0}} is a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in the human body. It has been created by the Human Metabolome Project funded by Genome Canada{{cite web|title=Human Metabolome Project|url=http://metabolomics.ca/|access-date=13 February 2013}} 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. 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,{{cite journal |title=DrugBank: a comprehensive resource for in silico drug discovery and exploration |last1=Wishart |first1=David S. |first2=Craig |last2=Knox |first3=An Chi |last3=Guo |first4=Savita |last4=Shrivastava |first5=Murtaza |last5=Hassanali |first6=Paul |last6=Stothard |first7=Zhan |last7=Chang |first8=Jennifer |last8=Woolsey |journal=Nucleic Acids Research |date=January 1, 2006 |volume=34 |issue=D1 |pages=D668–D672 |doi=10.1093/nar/gkj067 |pmid=16381955 |pmc=1347430}}{{cite journal |title=DrugBank: a knowledgebase for drugs, drug actions and drug targets|last=Wishart|first=DS|author2=Knox C |author3=Guo AC |journal=Nucleic Acids Research|date=Jan 2008|volume=36|issue=Database issue|pages=D901-6|doi=10.1093/nar/gkm958|pmid=18048412|pmc=2238889|display-authors=etal}}{{cite journal |title=DrugBank 3.0: a comprehensive resource for 'omics' research on drugs.|last=Knox|first=C |author2=Law, V |author3=Jewison, T |author4=Liu, P |author5=Ly, S |author6=Frolkis, A |author7=Pon, A |author8=Banco, K |author9=Mak, C |author10=Neveu, V |author11=Djoumbou, Y |author12=Eisner, R |author13=Guo, AC |author14=Wishart, DS.|journal=Nucleic Acids Research|date=Jan 2011|volume=39|issue=Database issue|pages=D1035-41|doi=10.1093/nar/gkq1126|pmid=21059682|pmc=3013709}} T3DB,{{cite journal |title=T3DB: a comprehensively annotated database of common toxins and their targets.|last=Lim|first=E|author2=Pon A |author3=Djoumbou Y |author4=Knox C |author5=Shrivastava S |author6=Guo AC |author7=Neveu V |author8=Wishart DS. |journal=Nucleic Acids Research|date=Jan 2010|volume=38|issue=Database issue|pages=D781-6|doi=10.1093/nar/gkp934|pmid= 19897546|pmc=2808899}} SMPDB {{cite journal |title=SMPDB: The Small Molecule Pathway Database.|last=Frolkis|first=A |author2=Knox, C |author3=Lim, E |author4=Jewison, T |author5=Law, V |author6=Hau, DD |author7=Liu, P |author8=Gautam, B |author9=Ly, S |author10=Guo, AC |author11=Xia, J |author12=Liang, Y |author13=Shrivastava, S |author14=Wishart, DS.|journal=Nucleic Acids Research|date=Jan 2010|volume=38|issue=Database issue|pages=D480-7|doi=10.1093/nar/gkp1002|pmid=19948758|pmc=2808928}} 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.