title: SMPDB: The Small Molecule Pathway Database.
abstract: The Small Molecule Pathway Database (SMPDB) is an interactive, visual database containing more than 350 small-molecule pathways found in humans. More than 2/3 of these pathways (>280) are not found in any other pathway database. SMPDB is designed specifically to support pathway elucidation and pathway discovery in clinical metabolomics, transcriptomics, proteomics and systems biology. SMPDB provides exquisitely detailed, hyperlinked diagrams of human metabolic pathways, metabolic disease pathways, metabolite signaling pathways and drug-action pathways. All SMPDB pathways include information on the relevant organs, organelles, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Each small molecule is hyperlinked to detailed descriptions contained in the Human Metabolome Database (HMDB) or DrugBank and each protein or enzyme complex is hyperlinked to UniProt. All SMPDB pathways are accompanied with detailed descriptions, providing an overview of the pathway, condition or processes depicted in each diagram. The database is easily browsed and supports full text searching. Users may query SMPDB with lists of metabolite names, drug names, genes/protein names, SwissProt IDs, GenBank IDs, Affymetrix IDs or Agilent 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. All of SMPDB's images, image maps, descriptions and tables are downloadable. SMPDB is available at: http://www.smpdb.ca.
authors: Department of Computing Science, University of Alberta, Edmonton, AB, Canada.
authors: Alex
authors: A
authors: Frolkis
authors: Craig
authors: C
authors: Knox
authors: Emilia
authors: E
authors: Lim
authors: Timothy
authors: T
authors: Jewison
authors: Vivian
authors: V
authors: Law
authors: David D
authors: DD
authors: Hau
authors: Phillip
authors: P
authors: Liu
authors: Bijaya
authors: B
authors: Gautam
authors: Son
authors: S
authors: Ly
authors: An Chi
authors: AC
authors: Guo
authors: Jianguo
authors: J
authors: Xia
authors: Yongjie
authors: Y
authors: Liang
authors: Savita
authors: S
authors: Shrivastava
authors: David S
authors: DS
authors: Wishart
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods* / Q000639:trends; D030541:Databases, Genetic; D030561:Databases, Nucleic Acid; D030562:Databases, Protein; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D020407:Internet; D008322:Mammals; D055442:Metabolome; D055432:Metabolomics; D004364:Pharmaceutical Preparations / Q000378:metabolism; D017434:Protein Structure, Tertiary; D015398:Signal Transduction; D012984:Software
chemical_list: D004364:Pharmaceutical Preparations