What is PathBank?
PathBank is an interactive, visual database containing more than 40 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana. The majority of these pathways are not found in any other pathway database. PathBank 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 metabolic, signalling, disease, drug, and physiological pathways. All PathBank pathways include information on the relevant organelles, 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 PathBank 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 PathBank with lists of metabolite names, drug names, genes/protein complex 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 complex concentration data can also be visualized through PathBank's mapping interface. All of PathBank's images, image maps, descriptions, and tables are downloadable in several formats.
The PathBank 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. PathBank may be browsed by pathway, chemical compound, and protein complex. The pathway browse view generates a tabular synopsis of PathBank'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 its corresponding pathway button brings up a full-screen image for the selected pathway. Once opened, the pathway image may be navigated using the zoom and scroll buttons. As with most pathway databases, all of the chemical structures and proteins illustrated in PathBank's diagrams are hyperlinked to other online databases or tables. PathBank pathways can be visualized with full colour and detail or simplified into a black and white diagram with nodes and edges. Users may download pathways in image (SVG, PNG) and textual data exchange formats (BioPAX, SBGN, SBML, PWML), as well as chemical compound and protein complex information (including structures and sequences) on the downloads page.
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 PathBank 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.
PathBank'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 PathBank 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 PathBank. The Sequence Search button allows users to conduct BLASTP (protein complex) sequence searches of the protein complex sequences contained in PathBank. Both single and multiple sequence (i.e. whole proteome) BLAST queries are supported.