SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database

By Timothy Jewison, Yilu Su, Fatemeh Miri Disfany, Yongjie Liang, Craig Knox, Adam Maciejewski, Jenna Poelzer, Jessica Huynh, You Zhou, David Arndt and 10 more. Nucleic Acids Res., 2013

411 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/631c31b63338c726c1b4cebd0492e74f5d9ba6dc

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Citations in the corpus

HMDB 4.0: the human metabolome database for 2018 (2017, background): “0 (30), which is now fully linked to HMDB.”
MetaboAnalyst 3.0—making metabolomics more meaningful (2015, background): “Substantial updates to MetaboAnalyst’s compound library and metabolic pathways library based on the latest versions of HMDB (16), SMPDB (17) and KEGG (18); 4.”
MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis (2018, methodology): “The inclusion of SMPDB pathways for other model organisms will occur in the next few months (25).”
Using clusterProfiler to characterize multiomics data (2024, positive): “If you use the feature ID from another common database, such as Enzyme Commission (EC) numbers 50 , Human Metabolome Database (HMDB) 51 or the Small Molecule Pathway Database (SMPDB) 52 , you can use an in-house developed package, MicrobiomeProfiler, which provides enrichKO, enrichHMDB and enrichSMP”
Metabolomics for Investigating Physiological and Pathophysiological Processes. (2019, methodology): “When combined with additional biological knowledge found in pathway databases (143, 219, 225) or when processed using tools such as metabolite set enrichment analysis (523, 524) and biological network modeling (272), these data can be used to gain key insights into how certain metabolites contribute”