Automated Drawing of Metabolic Pathways

Abstract

The EcoCyc system consists of a knowledge base that describes the genes and intermediary metabolism of E. coli, and a graphical user interface (GUI) for accessing that knowledge. This paper presents algorithms for drawing metabolic pathways by dynamically querying the underlying knowledge base. These algorithms provide a foundation for building graphical user interfaces to metabolic databases. Pathway drawing is a graph-layout problem. Our algorithms draw pathways of several different topologies, including linear, cyclic, and branching pathways, as well as larger groupings of such pathways. The algorithms provide several visual presentations of metabolic pathways, for example, compounds can be drawn as names and/or chemical structures, and enzyme names and side compounds can be drawn or omitted. The GUI also provides several facilities for navigating in the space of biochemical pathways, such as traversing connections between pathways, and exploding or collapsing a pathway to include or exclude neighboring pathways.