title: SMPDB 2.0: big improvements to the Small Molecule Pathway Database.
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 >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.
authors.affiliation: Department of Computing Science, University of Alberta, Edmonton, AB, Canada T6G 2E8, Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E8 and National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, AB, Canada T6G 2M9.
authors.forename: Timothy
authors.initials: T
authors.lastname: Jewison
authors.forename: Yilu
authors.initials: Y
authors.lastname: Su
authors.forename: Fatemeh Miri
authors.initials: FM
authors.lastname: Disfany
authors.forename: Yongjie
authors.initials: Y
authors.lastname: Liang
authors.forename: Craig
authors.initials: C
authors.lastname: Knox
authors.forename: Adam
authors.initials: A
authors.lastname: Maciejewski
authors.forename: Jenna
authors.initials: J
authors.lastname: Poelzer
authors.forename: Jessica
authors.initials: J
authors.lastname: Huynh
authors.forename: You
authors.initials: Y
authors.lastname: Zhou
authors.forename: David
authors.initials: D
authors.lastname: Arndt
authors.forename: Yannick
authors.initials: Y
authors.lastname: Djoumbou
authors.forename: Yifeng
authors.initials: Y
authors.lastname: Liu
authors.forename: Lu
authors.initials: L
authors.lastname: Deng
authors.forename: An Chi
authors.initials: AC
authors.lastname: Guo
authors.forename: Beomsoo
authors.initials: B
authors.lastname: Han
authors.forename: Allison
authors.initials: A
authors.lastname: Pon
authors.forename: Michael
authors.initials: M
authors.lastname: Wilson
authors.forename: Shahrzad
authors.initials: S
authors.lastname: Rafatnia
authors.forename: Philip
authors.initials: P
authors.lastname: Liu
authors.forename: David S
authors.initials: DS
authors.lastname: Wishart
mesh_terms: D003196:Computer Graphics; D062126:Databases, Chemical; D006801:Humans; D020407:Internet; D008659:Metabolic Diseases / Q000378:metabolism; D053858:Metabolic Networks and Pathways; D004364:Pharmaceutical Preparations / Q000378:metabolism; D011506:Proteins / Q000737:chemistry / Q000378:metabolism
chemical_list: D004364:Pharmaceutical Preparations; D011506:Proteins