About the Pathway Tools WWW Server

The Pathway Tools WWW Server allows users to query one or more Pathway/Genome Databases, such as the EcoCyc database, through the WWW. This page explains the query functionality supported by the Pathway Tools WWW server.

Each Pathway/Genome Database contains information about genes, proteins, and pathways for a single organism. The Pathway Tools WWW server allow users to retrieve and visualize information about these database objects. When formulating a query, consider first what type of object you wish to query (such as a gene or a metabolic pathway), and then consider how to find that particular object. Several query strategies are supported.

Once you retrieve a given object you can navigate to related objects in the WWW page by clicking on the names of those objects the graphical portion of the diagram, or by clicking on the highlighted objects in the textual portion of the diagram. For example, in pathway drawings, the compound and enzyme names are clickable, as are the reaction arrows. In genomic map drawings, the gene names are clickable, as are the tick marks along the DNA strand (clicking on a tick mark zooms in on a region of the map).

Two types of query access are provided to the WWW server:

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