SMPDB: The Small Molecule Pathway Database

By A. Frolkis, Craig Knox, Emilia Lim, Timothy Jewison, V. Law, D. Hau, Philip Liu, Bijaya Gautam, Son Ly, Anchi Guo and 4 more. Nucleic Acids Res., 2009

343 citations recorded by the source corpus.

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.

Subfields: Computational Theory and Mathematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/52a56e3bc6dc4d5ed0b9558baf340e4ab99909a2

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Citations in the corpus

The enumeration of chemical space (2012, neutral): “13 Smaller, more specialized databases are also available, such as the NCI open database, 14 ChemDB, 15 BindingDB, 16 , 17 ChemBank, 18 ChEMBL, 19 , 20 CTD, 21 HMBD, 22 SMPBD, 23 and DrugBank (Table 1).”
T3DB: the toxic exposome database (2014, background): “These include the addition of a ‘Biological Properties’ section covering a toxin’s status (detected/quantified), origin (exogenous/endogenous), cellular locations, biofluid locations, tissue locations and pathways (SMPDB (23) or KEGG).”
HMDB 3.0—The Human Metabolome Database in 2013 (2012, background): “Since then, these early pathway diagrams have been substantially upgraded in terms of quality, quantity and viewability, particularly through the inclusion of our own SMPDB pathways (14).”
DrugBank 4.0: shedding new light on drug metabolism (2013, methodology): “In addition, DrugBank now offers comprehensive, colorful, manually drawn interactive drug metabolism pathways [using the SMPDB pathway model (13)] for >50 drugs.”
Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review (2012, background): “…Caspi et al., 2012 HumanCyc http://humancyc.org Romero et al., 2005 SMPDB Small Molecule (e.g., drug) Pathway Database http://smpdb.ca Frolkis et al., 2010 HMDB Human Metabolome Database http://hmdb.ca Wishart et al., 2009 BRENDA Comprehensive enzyme data resource…”
DrugBank 3.0: a comprehensive resource for ‘Omics’ research on drugs (2010, methodology): “This tight integration between DrugBank and SMPDB should allow researchers to visualize the ‘big picture’ with respect to drugs and how they act or how they are processed in the body.”
The ConsensusPathDB interaction database: 2013 update (2012, background): “The newly integrated resources are BIND (protein–protein interactions) (10), DrugBank (drug–target interactions) (11), InnateDB (protein–protein, biochemical and gene regulatory interactions) (12), MatrixDB (protein–protein interactions) (13), PDZBase (protein–protein interactions) (14), PhosphoPOIN”
Using MetaboAnalyst 3.0 for Comprehensive Metabolomics Data Analysis (2016, neutral): “Users can follow the link to browse the detailed pathway map within SMPDB. 6.”
SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database (2013, methodology): “In an effort to make web-based biological pathway data more visually appealing and physiologically relevant, particularly for biomedical applications, we developed the Small Molecule Pathway Database or SMPDB (7).”
MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data (2010, background): “Metabolites associated with diﬀerent diseases were manually identiﬁed, merged and subsequently reﬁned by reading the original publications listed in the Human Metabolome Database (HMDB) (18), the Metabolic Information Center (MIC), and SMPDB.”
The Human Urine Metabolome (2013, background): “These maps are intended to help users visualize the chemical structures on metabolic pathways and to get detailed information about metabolic processes [55].”
MetaboAnalyst 2.0—a comprehensive server for metabolomic data analysis (2012, background): “The latter two modules are based on literature-derived knowledge, specialized metabolic pathway databases [such as SMPDB (10)] and richly annotated metabolite databases [such as HMDB (11)].”