In recent years, the number of pathway databases has been increasing. This is due largely to the emergence of a variety of novel experimental and computational methods for generating pathway data on a high throughput scale. It is difficult to gather pathway information from these varied sources for analysis.
A standard exchange format for pathway data would allow pathway databases to provide their data in a common form, thus significantly reducing the amount of time and energy spent by the bioinformatics community on data integration. BioPAX (http://www.biopax.org ) is a new community-based effort to develop a technical recommendation for a biological pathways data exchange format. The format is being designed to represent data from diverse sources such as aMAZE, BIND, BioCyc, and WIT.
In designing BioPAX, we endeavor to balance the many different representational needs of the biological pathways community by remaining flexible and extensible. A draft ontology will soon be available that provides a simple framework for the exchange format. This framework will be extended to include more detail via a leveled approach similar to that used by SBML. Encapsulation and compatibility are also being emphasized in the design, as is the use of existing standards, such as the Gene Ontology, when available.
An initial implementation of BioPAX will soon be available in both OWL and XML Schema versions. The development process is open for comment and feedback and participation of all interested parties is encouraged.