The Pathway Browser provides a tree-structured view of the metabolic pathways, and signaling pathways available in the database. Metabolic pathways, processes, and molecular entities can be browsed in different orders (Figure 2-a), and a set of useful queries can be specified about pathways, processes and molecular entities, from predefined simple queries to parameterized path selection and neighborhood queries. Similarly, for signaling pathways, signaling steps, and signaling and signaled molecules and their components can be browsed; a set of useful queries for signaling pathways are presently being developed (Figure 2-b). When one right-clicks on a tree node, dynamic context menus will popup, which leads to a set of functionalities. For more details about the Pathway Browser, see [KL03].
Figure 2. Metabolic Pathway Browser (a) and Signaling Pathway Browser (b).
The Pathway Viewer presently visualizes a single metabolic pathway (Figure 3) or multiple metabolic pathways in an organism-specific or organism-independent manner, provides a large number of functionalities including collapsing-zooming, hiding-expanding, editing, and node property-setting. The tool supports ad-hoc querying of the pathways data as well as menu-driven queries. It also provides a seamless transition from metabolic pathways to signaling pathways, and from signaling steps that belong to metabolic pathway processes into the relevant pathways. Pathway viewer for signaling pathways is currently under construction. For more details on the Pathway Viewer, see the Pathway Viewer user manual.
Figure 3. Pathway Viewer. The middle pane is the main display window for the pathway graph. The right pane is the Genome Viewer, which displays genes for the enzymes used in the pathway in the middle pane. The left pane is the Overview window and Property window for graph objects. The Genome Viewer and the Overview/Property pane can be hidden or unhidden as needed.
