The Small Molecule Pathway Database (SMPDB)[1][2] is a comprehensive, high-quality, freely accessible, online database containing more than 600 small molecule (i.e. metabolic) pathways found in humans. SMPDB is designed specifically to support pathway elucidation and pathway discovery in metabolomics, transcriptomics, proteomics and systems biology. It is able to do so, in part, by providing colorful, detailed, fully searchable, hyperlinked diagrams of five types of small molecule pathways: 1) general human metabolic pathways; 2) human metabolic disease pathways; 3) human metabolite signaling pathways; 4) drug-action pathways and 5) drug metabolism pathways. SMPDB pathways may be navigated, viewed and zoomed interactively using a Google Maps-like interface. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures (Fig. 1). Each small molecule in SMPDB is hyperlinked to detailed descriptions contained in the HMDB[3] or DrugBank[4] and each protein or enzyme complex is hyperlinked to UniProt.[5] Additionally, all SMPDB pathways are accompanied with detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram. Users can browse the SMPDB (Fig. 2) or search its contents by text searching (Fig. 3), sequence searching, or chemical structure searching. More powerful queries are also possible including searching with lists of gene or protein names, drug names, metabolite names, GenBank IDs, Swiss-Prot IDs, Agilent or Affymetrixmicroarray IDs. These queries will produce lists of matching pathways and highlight the matching molecules on each of the pathway diagrams. Gene, metabolite and protein concentration data can also be visualized through SMPDB's mapping interface.
SMPDB
Content
Description
Pathway database
Data types captured
Small molecule pathways, metabolic pathways, metabolic disease pathways, metabolite signaling pathways, drug action pathways, drug metabolism pathways
The first version of SMPDB was released on January 1, 2010.[1] This release contained more than 350 image-mapped pathways for small molecule pathways. The viewer interface was limited to scroll-bar image navigation with 3-step (small, medium, large) zooming. The pathways in this first version were limited to 1) human metabolic pathways; 2) human metabolic disease pathways; and 3) human metabolite signaling pathways. The second version of SMPDB was released in 2014.[2] This version contained more than 620 small molecule pathways. The viewer interface was enhanced to include a Google-Map-like interface with click-n-drag image navigation and unlimited, interactive zooming. The pathways in this second version were expanded to include: 1) general human metabolic pathways; 2) human metabolic disease pathways; 3) human metabolite signaling pathways; 4) drug action pathways and 5) drug metabolism pathways.
^UniProt Consortium (Jan 2011). "Ongoing and future developments at the Universal Protein Resource". Nucleic Acids Research. 39 (Database issue): D214-9. doi:10.1093/nar/gkq1020. PMC3013648. PMID 21051339.
April 15, 2024
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The Small Molecule Pathway Database SMPDB 1 2 is a comprehensive high quality freely accessible online database containing more than 600 small molecule i e metabolic pathways found in humans SMPDB is designed specifically to support pathway elucidation and pathway discovery in metabolomics transcriptomics proteomics and systems biology It is able to do so in part by providing colorful detailed fully searchable hyperlinked diagrams of five types of small molecule pathways 1 general human metabolic pathways 2 human metabolic disease pathways 3 human metabolite signaling pathways 4 drug action pathways and 5 drug metabolism pathways SMPDB pathways may be navigated viewed and zoomed interactively using a Google Maps like interface All SMPDB pathways include information on the relevant organs subcellular compartments protein cofactors protein locations metabolite locations chemical structures and protein quaternary structures Fig 1 Each small molecule in SMPDB is hyperlinked to detailed descriptions contained in the HMDB 3 or DrugBank 4 and each protein or enzyme complex is hyperlinked to UniProt 5 Additionally all SMPDB pathways are accompanied with detailed descriptions and references providing an overview of the pathway condition or processes depicted in each diagram Users can browse the SMPDB Fig 2 or search its contents by text searching Fig 3 sequence searching or chemical structure searching More powerful queries are also possible including searching with lists of gene or protein names drug names metabolite names GenBank IDs Swiss Prot IDs Agilent or Affymetrix microarray IDs These queries will produce lists of matching pathways and highlight the matching molecules on each of the pathway diagrams Gene metabolite and protein concentration data can also be visualized through SMPDB s mapping interface SMPDBContentDescriptionPathway databaseData typescapturedSmall molecule pathways metabolic pathways metabolic disease pathways metabolite signaling pathways drug action pathways drug metabolism pathwaysContactResearch centerUniversity of Alberta and The Metabolomics Innovation CentreLaboratoryDavid S WishartPrimary citationSMPDB The Small Molecule Pathway Database 1 AccessWebsitehttp www smpdb caDownload URLhttp www smpdb ca downloadsMiscellaneousData releasefrequencyEvery 2 3 years with periodic corrections and updatesCuration policyManually curatedSMPDB is part of a suite of metabolomics databases that also includes Human Metabolome Database DrugBank and the Toxin and Toxin Target Database T3DB While DrugBank includes information on 7000 drugs and gt 4200 non redundant drug targets enzymes transporters and carriers HMDB houses over 40 000 small molecule metabolites found in the human body The suite is complemented by T3DB with its over 3100 common toxic substances and over 1300 corresponding toxin targets Version History editThe first version of SMPDB was released on January 1 2010 1 This release contained more than 350 image mapped pathways for small molecule pathways The viewer interface was limited to scroll bar image navigation with 3 step small medium large zooming The pathways in this first version were limited to 1 human metabolic pathways 2 human metabolic disease pathways and 3 human metabolite signaling pathways The second version of SMPDB was released in 2014 2 This version contained more than 620 small molecule pathways The viewer interface was enhanced to include a Google Map like interface with click n drag image navigation and unlimited interactive zooming The pathways in this second version were expanded to include 1 general human metabolic pathways 2 human metabolic disease pathways 3 human metabolite signaling pathways 4 drug action pathways and 5 drug metabolism pathways See also editKEGG HMDB DrugBank Reactome MetaCyc List of biological databasesReferences edit a b c 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 a b Jewison T Su Y Disfany FM et al Jan 2014 Small Molecule Pathway Database Nucleic Acids Research 42 Database issue D478 84 doi 10 1093 nar gkt1067 PMC 3965088 PMID 24203708 Wishart DS Tzur D Knox C Eisner R Guo AC Young N Cheng D Jewell K Arndt D Sawhney S Fung C Nikolai L Lewis M Coutouly MA Forsythe I Tang P Shrivastava S Jeroncic K Stothard P Amegbey G Block D Hau DD Wagner J Miniaci J Clements M Gebremedhin M Guo N Zhang Y Duggan GE Macinnis GD Weljie AM Dowlatabadi R Bamforth F Clive D Greiner R Li L Marrie T Sykes BD Vogel HJ Querengesser L Jan 2007 HMDB the Human Metabolome Database Nucleic Acids Research 35 Database issue D521 6 doi 10 1093 nar gkl923 PMC 1899095 PMID 17202168 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 UniProt Consortium Jan 2011 Ongoing and future developments at the Universal Protein Resource Nucleic Acids Research 39 Database issue D214 9 doi 10 1093 nar gkq1020 PMC 3013648 PMID 21051339 Retrieved from https en wikipedia org w index php title Small Molecule Pathway Database amp oldid 1197201002, wikipedia, wiki, book, books, library,
