Small Molecule Pathway Database (SMPDB)

Category Metabolomics/Metabonomics>Knowledge Bases/Databases/Tools and Cross-Omics>Pathway Knowledge Bases/Databases/Tools

Abstract SMPDB (The Small Molecule Pathway Database) is an interactive, visual database containing more than 350 small molecule pathways found in humans.

More than 2/3 of these pathways (greater than 280) are Not currently found in any other pathway database. SMPDB is designed specifically to support pathway elucidation and pathway discovery in metabolomics, transcriptomics, and proteomics and systems biology.

It is able to do so, in part, by providing 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 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 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 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 interface --

The SMPDB interface is modeled to some extent after the interface used for DrugBank and the HMDB with a navigation panel for Browsing, Searching and Downloading the database.

Below the navigation panel is a simple text query box that supports general text queries of the entire textual component of the database. Mousing over the Browse button allows users to choose between two (2) browsing options, SMP-BROWSE and SMP-MAP.

1) Small Molecule Pathway (SMP)-BROWSE -

SMP-BROWSE 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 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 expanded by clicking on the Zoom button located at the top and bottom of the image. As with most pathway databases, all of the chemical structures and proteins/enzymes illustrated in SMPDB’s diagrams are hyperlinked to other on-line databases or tables.

Specifically, all metabolites, drugs or proteins shown in the SMP-BROWSE tables or in a pathway diagram are linked to HMDB, DrugBank or UniProt, respectively (as stated above…). Therefore, clicking on chemical or protein image will open a new browser window with the corresponding DrugCard, MetaboCard or UniProt table being displayed.

By hyper-linking to these particular databases, SMPDB is able to provide considerably more information about its small molecules and its proteins.

Indeed, SMPDB’s UniProt links provide an average of 40 data fields about each protein, including nomenclature, function, reaction and structural information, while SMPDB’s DrugBank/HMDB links provide an average of 100 data fields about each compound, including detailed descriptions;

extensive nomenclature information, comprehensive physico-chemical data, reference Nuclear Magnetic Resonance (NMR) and mass spectrometry (MS) spectra as well as extensive information about tissue or biofluid locations and concentrations.

2) Small Molecule Pathway (SMP)-MAP -

In contrast to SMP-BROWSE, which is used for data browsing and single entity highlighting, 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, and protein names, UniProt IDs, GenBank IDs, Agilent IDs or Affymetrix IDs and to have a table generated of pathways containing those components.

The resulting table, like the SMP-BROWSE table, displays a thumbnail image of the matching pathways along with the list of matching components (metabolites, drugs, proteins, 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, proteins, etc.) highlighted in red.

Through SMP-MAP, SMPDB is also able to support pathway elucidation and pathway discovery in a variety of clinical ‘omics’ studies.

For instance, users may assemble lists of significantly altered metabolites (or metabolite identifiers), genes (or gene identifiers) or proteins (or protein identifiers) from clinical metabolomic, microarray or proteomic studies.

The resulting lists, scores and color-coded pathways can allow the identification or diagnostic confirmation of certain diseases, the association of certain ‘omic’ signatures with specific pathways or the discovery of pathway and/or disease associations that had Not previously been detected.

By allowing users to explore each high-scoring pathway individually, SMP-MAP may also allow new biochemical insights to be gained or suggest new confirmatory clinical tests to be performed.

SMPDB’s Search menu -

SMPDB’s Search menu offers users a choice of searching the database by chemical structure (ChemQuery), text (TextQuery) or sequence (SeqSearch).

The ChemQuery option allows users to draw [using the MarvinSketch applet - MarvinSketch is an advanced chemical editor for drawing chemical structures, queries and reactions.

It has a rich (and growing) list of editing features, is chemically aware and is able to call ChemAxon’s structure based calculation plug-ins for structures on the canvas] 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 SeqSearch button allows users to conduct BLASTP (protein) sequence searches of the protein sequences contained in SMPDB. Both single and multiple sequence (i.e. whole proteome) BLAST queries are supported.

Users may download selected text components and sequence data from SMPDB by clicking on the File Downloads button. Users can also download pathway images and PowerPoint’s by clicking on the Pathway Downloads button.

System Requirements

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Manufacturer Web Site Small Molecule Pathway Database (SMPDB)

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G6G Abstract Number 20666

G6G Manufacturer Number 104124