The Pathway Editor: A tool for managing complex biological networks

Abstract

Biological networks are systems of biochemical processes inside a cell that involve cellular constituents such as DNA, RNA, proteins, and various small molecules. Pathway maps are often used to represent the structure of such networks with associated biological information. Several pathway editors exist, and they vary according to specific domains of knowledge. This paper presents a review of existing pathway editors, along with an introduction to the Edinburgh Pathway Editor (EPE). EPE was designed for the annotation, visualization, and presentation of a wide variety of biological networks that include metabolic, genetic, and signal transduction pathways. EPE is based on a metadata-driven architecture. The editor supports the presentation and annotation of maps, in addition to the storage and retrieval of reaction kinetics information in relational databases that are either local or remote. EPE also has facilities for linking graphical objects to external databases and Web resources, and is capable of reproducing most existing graphical notations and visual representations of pathway maps. In summary, EPE provides a highly flexible tool for combining visualization, editing, and database manipulation of information relating to biological networks. EPE is open-source software, distributed under the Eclipse open-source application platform license.