SMPDB 2.0: big improvements to the Small Molecule Pathway Database. Jewison, T., Su, Y., Disfany, F. M., Liang, Y., Knox, C., Maciejewski, A., Poelzer, J., Huynh, J., Zhou, Y., Arndt, D., Djoumbou, Y., Liu, Y., Deng, L., Guo, A. C., Han, B., Pon, A., Wilson, M., Rafatnia, S., Liu, P., & Wishart, D. S. Nucleic Acids Research, 42(Database issue):D478–484, January, 2014. doi abstract bibtex The 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 \textgreater600 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 \textgreater70%. 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.
@article{jewison_smpdb_2014,
title = {{SMPDB} 2.0: big improvements to the {Small} {Molecule} {Pathway} {Database}},
volume = {42},
issn = {1362-4962},
shorttitle = {{SMPDB} 2.0},
doi = {10.1093/nar/gkt1067},
abstract = {The 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 {\textgreater}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 {\textgreater}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.},
language = {eng},
number = {Database issue},
journal = {Nucleic Acids Research},
author = {Jewison, Timothy and Su, Yilu and Disfany, Fatemeh Miri and Liang, Yongjie and Knox, Craig and Maciejewski, Adam and Poelzer, Jenna and Huynh, Jessica and Zhou, You and Arndt, David and Djoumbou, Yannick and Liu, Yifeng and Deng, Lu and Guo, An Chi and Han, Beomsoo and Pon, Allison and Wilson, Michael and Rafatnia, Shahrzad and Liu, Philip and Wishart, David S.},
month = jan,
year = {2014},
pmid = {24203708},
pmcid = {PMC3965088},
keywords = {Computer Graphics, Databases, Chemical, Humans, Internet, Metabolic Diseases, Metabolic Networks and Pathways, Pharmaceutical Preparations, Proteins},
pages = {D478--484},
}
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SMPDB contains \\textgreater600 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 \\textgreater70%. 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. 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