Biology:Human Metabolome Database

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Short description: Database of human metabolites
Human Metabolome Database
Human Metabolome Database logo.png
Content
DescriptionMetabolomics 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
Contact
Research centreUniversity of Alberta and The Metabolomics Innovation Centre
LaboratoryDavid S. Wishart
Primary citationHMDB: the Human Metabolome Database.[1]
Access
Websitehttp://www.hmdb.ca
Download URLhttp://www.hmdb.ca/downloads
Miscellaneous
Data release
frequency		Every 2 years with monthly corrections and updates
Curation policyManually curated

The Human Metabolome Database (HMDB)[1][2][3][4] 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 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.

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
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 0 279 884 7,418 11,493
Number of human-specific pathway maps 26 58 442 − −
Number of compounds in Human Metabolome Library 607 920 1,031 − −
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

References

  1. ↑ 1.0 1.1 1.2 Wishart, David S.; Tzur, Dan; Knox, Craig; Eisner, Roman; Guo, An Chi; Young, Nelson; Cheng, Dean; Jewell, Kevin et al. (January 1, 2007). "HMDB: the Human Metabolobe Database" (PDF). Nucleic Acids Research 35 (D1): D521-D526. doi:10.1093/nar/gkl923. PMID 17202168. PMC 1899095. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899095/pdf/gkl923.pdf. 
  2. ↑ 2.0 2.1 Wishart, David S.; Knox, Craig; Guo, An Chi; Eisner, Roman; Young, Nelson; Gautam, Bijaya; Hau, David D.; Psychogios, Nick et al. (January 1, 2009). "HMDB: a knowledgebase for the human metabolome" (PDF). Nucleic Acids Research 37 (D1): D603-D610. doi:10.1093/nar/gkn810. PMID 18953024. PMC 2686599. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686599/pdf/gkn810.pdf. 
  3. ↑ Forsythe, Ian J.; Wishart, David S. (March 1, 2009). "Exploring Human Metabolites Using the Human Metabolome Database". Current Protocols in Bioinformatics 25: 14.8.1–14.8.45. doi:10.1002/0471250953.bi1408s25. ISBN 978-0471250951. PMID 19274632. 
  4. ↑ 4.0 4.1 Wishart, David S.; Jewison, Timothy; Guo, An Chi; Wilson, Michael; Knox, Craig; Liu, Yifeng; Djombou Feunang, Yannick; Mandal, Rupasri et al. (January 1, 2013). "HMDB 3.0—The Human Metabolobe Database in 2013" (PDF). Nucleic Acids Research 41 (D1): D801-D807. doi:10.1093/nar/gks1065. PMID 23161693. PMC 3531200. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531200/pdf/gks1065.pdf. 
  5. ↑ 5.0 5.1 "Human Metabolome Project". http://metabolomics.ca/. 
  6. ↑ Wishart, David S.; Knox, Craig; Guo, An Chi; Shrivastava, Savita; Hassanali, Murtaza; Stothard, Paul; Chang, Zhan; Woolsey, Jennifer (January 1, 2006). "DrugBank: a comprehensive resource for in silico drug discovery and exploration". Nucleic Acids Research 34 (D1): D668–D672. doi:10.1093/nar/gkj067. PMID 16381955. 
  7. ↑ Wishart, DS et al. (Jan 2008). "DrugBank: a knowledgebase for drugs, drug actions and drug targets". Nucleic Acids Research 36 (Database issue): D901-6. doi:10.1093/nar/gkm958. PMID 18048412. 
  8. ↑ Knox, C; Law, V; Jewison, T; Liu, P; Ly, S; Frolkis, A; Pon, A; Banco, K et al. (Jan 2011). "DrugBank 3.0: a comprehensive resource for 'omics' research on drugs.". Nucleic Acids Research 39 (Database issue): D1035-41. doi:10.1093/nar/gkq1126. PMID 21059682. 
  9. ↑ Lim, E; Pon A; Djoumbou Y; Knox C; Shrivastava S; Guo AC; Neveu V; Wishart DS. (Jan 2010). "T3DB: a comprehensively annotated database of common toxins and their targets.". Nucleic Acids Research 38 (Database issue): D781-6. doi:10.1093/nar/gkp934. PMID 19897546. 
  10. ↑ Frolkis, A; Knox, C; Lim, E; Jewison, T; Law, V; Hau, DD; Liu, P; Gautam, B et al. (Jan 2010). "SMPDB: The Small Molecule Pathway Database.". Nucleic Acids Research 38 (Database issue): D480-7. doi:10.1093/nar/gkp1002. PMID 19948758. 
  11. ↑ 11.0 11.1 "Human Metabolome Database Release Notes". http://www.hmdb.ca/release-notes. 
  12. ↑ Wishart, David S.; Djombou Feunang, Yannick; Marcu, Ana; Guo, An Chi; Liang, Kevin; Vázquez Fresno, Rosa; Sajed, Tanvir; Johnson, Daniel et al. (January 4, 2018). "HMDB 4.0: the human metabolome database for 2018" (PDF). Nucleic Acids Research 46 (D1): D608-D617. doi:10.1093/nar/gkx1089. PMID 29140435. PMC 5753273. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753273/pdf/gkx1089.pdf. 



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