Human Metabolome Database

From Wikipedia, the free encyclopedia

Template:Short description Script error: No such module "about".

Page Module:Infobox/styles.css has no content.

Human Metabolome Database
Lua error in package.lua at line 80: module 'Module:InfoboxImage/data' not found.
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 centerUniversity 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 online database of small molecule metabolites 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] toxin database,[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 Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting".
Number of unique metabolite synonyms Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting".
Number of compounds with disease links Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting".
Number of compounds with biofluid or tissue concentration data Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting".
Number of compounds with chemical synthesis references Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting".
Number of compounds with experimental reference 1H and or 13C NMR spectra Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting".
Number of compounds with reference MS/MS spectra Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting".
Number of compounds with reference GC-MS reference data Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting".
Number of human-specific pathway maps Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting".
Number of compounds in Human Metabolome Library Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting".
Number of HMDB data fields Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting".
Number of predicted molecular properties Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting". Script error: No such module "Number table sorting".

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

Page Template:Reflist/styles.css has no content.

  1. ^ a b c Template:Cite HMDB
  2. ^ a b Template:Cite HMDB
  3. ^ Page Module:Citation/CS1/styles.css has no content.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. S2CID 24291704.
  4. ^ a b Template:Cite HMDB
  5. ^ a b Page Module:Citation/CS1/styles.css has no content."Human Metabolome Project". Retrieved 13 February 2013.
  6. ^ Page Module:Citation/CS1/styles.css has no content.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. PMC 1347430. PMID 16381955.
  7. ^ Page Module:Citation/CS1/styles.css has no content.Wishart, DS; Knox C; Guo AC; 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. PMC 2238889. PMID 18048412.
  8. ^ Page Module:Citation/CS1/styles.css has no content.Knox, C; Law, V; Jewison, T; Liu, P; Ly, S; Frolkis, A; Pon, A; Banco, K; Mak, C; Neveu, V; Djoumbou, Y; Eisner, R; Guo, AC; Wishart, DS. (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. PMC 3013709. PMID 21059682.
  9. ^ Page Module:Citation/CS1/styles.css has no content.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. PMC 2808899. PMID 19897546.
  10. ^ Page Module:Citation/CS1/styles.css has no content.Frolkis, A; Knox, C; Lim, E; Jewison, T; Law, V; Hau, DD; Liu, P; Gautam, B; Ly, S; Guo, AC; Xia, J; Liang, Y; Shrivastava, S; Wishart, DS. (Jan 2010). "SMPDB: The Small Molecule Pathway Database". Nucleic Acids Research. 38 (Database issue): D480-7. doi:10.1093/nar/gkp1002. PMC 2808928. PMID 19948758.
  11. ^ a b Page Module:Citation/CS1/styles.css has no content."Human Metabolome Database Release Notes".
  12. ^ Template:Cite HMDB

Lua error in package.lua at line 80: module 'Module:Navbox/configuration' not found.

Retrieved from "https://cosmopedia.co/index.php?title=Human_Metabolome_Database&oldid=10701986"