SMPDB 2.0: big improvements to the small molecule pathway database

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DOIResolve DOI: http://doi.org/10.1093/nar/gkt1067
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TypeArticle
Journal titleNucleic Acids Research
ISSN0305-1048
Volume42
IssueD1
PagesD478D484
AbstractThe Small Molecule Pathway Database (SMPDB, http://www.smpdb.ca) is a comprehensive, colorful, fully searchable and highly interactive database for visualizing human metabolic, drug action, drug metabolism, physiological activity and metabolic disease pathways. SMPDB contains >600 pathways with nearly 75% of its pathways not found in any other database. All SMPDB pathway diagrams are extensively hyperlinked and include detailed information on the relevant tissues, organs, organelles, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Since its last release in 2010, SMPDB has undergone substantial upgrades and significant expansion. In particular, the total number of pathways in SMPDB has grown by >70%. Additionally, every previously entered pathway has been completely redrawn, standardized, corrected, updated and enhanced with additional molecular or cellular information. Many SMPDB pathways now include transporter proteins as well as much more physiological, tissue, target organ and reaction compartment data. Thanks to the development of a standardized pathway drawing tool (called PathWhiz) all SMPDB pathways are now much more easily drawn and far more rapidly updated. PathWhiz has also allowed all SMPDB pathways to be saved in a BioPAX format. Significant improvements to SMPDB's visualization interface now make the browsing, selection, recoloring and zooming of pathways far easier and far more intuitive. Because of its utility and breadth of coverage, SMPDB is now integrated into several other databases including HMDB and DrugBank. © 2013 The Author(s). Published by Oxford University Press.
Publication date
LanguageEnglish
AffiliationNational Research Council Canada (NRC-CNRC); Security and Disruptive Technologies
Peer reviewedYes
NPARC number21270879
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Record identifiere305b799-2658-440d-ab04-3c7554ba7d28
Record created2014-02-17
Record modified2016-05-09
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