What is SMPDB?
SMPDB (The Small Molecule Pathway Database) is an interactive, visual database containing more than 700 small molecule pathways found in humans. Nearly 70% of these pathways (>400) are not found in any other pathway database. SMPDB is designed specifically to support pathway elucidation and pathway discovery in metabolomics, transcriptomics, proteomics and systems biology. It is able to do so, in part, by providing exquisitely detailed, fully searchable, 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, subcellular compartments, protein_complex cofactors, protein_complex locations, metabolite locations, chemical structures and protein_complex quaternary structures. Each small molecule is hyperlinked to detailed descriptions contained in the HMDB or DrugBank and each protein_complex or enzyme complex is hyperlinked to UniProt. All SMPDB pathways are accompanied with detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram. The database is easily browsed and supports full text, sequence and chemical structure searching. Users may query SMPDB with lists of metabolite names, drug names, genes/protein_complex names, SwissProt IDs, GenBank IDs. These queries will produce lists of matching pathways and highlight the matching molecules on each of the pathway diagrams. Gene, metabolite and protein_complex 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 also supported by The Metabolomics Innovation Centre, a Genome Canada-funded core facility serving the scientific community and industry with world-class expertise and cutting-edge technologies in metabolomics.
The SMPDB interface is modeled to some extent after the interface used for DrugBank and the HMDB with a navigation bar for browsing, searching and downloading the database. On the navigation bar is a simple text query box that supports general text queries of the entire textual component of the database. SMPDB may be browsed by pathway, chemicmal compound, and protein_complex. The pathway browse view generates a tabular synopsis of SMPDB's content with thumbnail images of the pathway diagrams, textual descriptions of the pathway, as well as lists of the corresponding chemical components and enzyme/protein_complex components. This browse view allows users to casually scroll through the database, select different pathway categories or re-sort its contents. Clicking on a given thumbnail image or the SMPDB pathway button brings up a full-screen image for the corresponding pathway. Once opened the pathway image may be navigated using on the zoom and scroll buttons. As with most pathway databases, all of the chemical structures and protein_complexes/enzymes illustrated in SMPDB's diagrams are hyperlinked to other on-line databases or tables.
SMP-MAP can be used for multiple entity highlighting and mapping. In particular, SMP-MAP allows users to enter lists of chemical names, gene names, protein_complex names, UniProt IDs, GenBank IDs, Agilent IDs or Affymetrix IDs and to have a table generated of pathways containing those components. The resulting table displays a thumbnail image of the matching pathways along with the list of matching components (metabolites, drugs, protein_complexes, etc.). The table is ordered by the number of matches, with the pathway having the most matches being at the top. Clicking on the thumbnail image or the SMPDB pathway button brings up a full-screen image for the corresponding pathway with all the matching components (metabolites, drugs, protein_complexes, etc.) highlighted in red. SMP-MAP is particularly useful for analyzing metabolomics, proteomics or transcriptomics data.
SMPDB's Search menu offers users a choice of searching the database by chemical structure (ChemQuery), text (TextQuery) or sequence (Sequence Search). The ChemQuery Structure Search option allows users to draw (using MarvinSketch applet) or write (using a SMILES string) a chemical compound and to search SMPDB for drugs and metabolites similar or identical to the query compound. The TextQuery button supports a more sophisticated text search (partial word matches, case sensitive, misspellings, etc.) of the text portion of SMPDB. The Sequence Search button allows users to conduct BLASTP (protein_complex) sequence searches of the protein_complex sequences contained in SMPDB. Both single and multiple sequence (i.e. whole proteome) BLAST queries are supported. Users may download pathways in image and textual data exchange formats, as well as chemical compound and protein_complex information (including structures and sequencse) on the downloads page.
SMPDB is offered to the public as a freely available resource. Use and re-distribution of the data, in whole or in part, for commercial purposes requires explicit permission of the authors and explicit acknowledgment of the source material (SMPDB) and the original publication (see below). We ask that users who download significant portions of the database cite the SMPDB paper in any resulting publications.
- Wishart DS, Frolkis A, Knox C, et al. SMPDB: The Small Molecule Pathway Database. Nucleic Acids Res. 2010 Jan;38(Database issue):D480-7.
- Jewison T, Su Y, Disfany FM, et al. SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database Nucleic Acids Res. 2014 Jan;42(Database issue):D478-84.