The Pathways Explorer is essentially a tool for querying the Pathways Database View. This tool presents a tree-structured interface that allows the user to explore the relationships between pathways, processes, molecules, and organisms.
A tree is a natural way of visualizing the graph-structured data in the Pathways Database since any given node in the graph (representing an object, such as a pathway, process, molecule, or organism) can be deemed the root, and any nodes connected to it by an edge can be considered its children. These children themselves may have children, and so on.
In the Pathways Explorer, each of these tree nodes can represent a specific instance of an object or many instances. For example, a node may represent the single process in the database with name X, a node may represent all processes in the database that are reversible, or a node may simply represent all processes in the database. Each of these tree object nodes has child nodes for each of its attributes. A node that is not an attribute can have any number of children. Also, there may be any number of top-level trees instantiated (i.e. the query-interface contains a forest of query trees).
To start the Pathway Explorer from the Pathway Browser interface, click on the Explorer tab (A). The initial state of the Pathways Explorer is shown in the figure below. The top row of buttons is always visible. The Run Query and Export Query buttons perform output queries. The Reset button brings you back to this empty tree Pathways Explorer, shown in the white area, is the root of the query tree. The Add buttons, children of the root, are used to insert objects into the query tree. Under the root may be added a Pathway, Process, Molecule or Organism.
