BioPAX - Biological Pathways Exchange Language Level 2, Version 1.0 Documentation

At present, there are over 215 Internet-accessible databases that store biological pathway data. Biologists often need to use information from many of these to support their research, but since each has its own representation conventions and data access methods, integrating data from multiple databases is very difficult. A widely-adopted biological pathway data exchange format will help. BioPAX (Biological Pathway Exchange - http://www.biopax.org) enables the integration of diverse pathway resources by defining an open file format specification for the exchange of biological pathway data. By utilizing the BioPAX format, the problem of data integration reduces to a semantic mapping between the data models of each resource and the data model defined by BioPAX. Widespread adoption of BioPAX for data exchange will increase access to and uniformity of pathway data from varied sources, thus increasing the efficiency of computational pathway research. This document describes BioPAX Level 2, which expands the scope of BioPAX to include representation of molecular binding interactions, protein post-translational modifications, basic experimental descriptions, and hierarchical pathways. Adding coverage of these features will allow BioPAX to represent the bulk of the data in the PSI-MI Level 2 format (http://psidev.sourceforge.net/mi/rel2/doc/) and lays the groundwork for better support of signal transduction and molecular states.