BioPAX is a standard, community-developed language for the description of biological pathways. It aims the facilitate the integration, exchange, and analysis of detail-rich pathway data. We have also developed a related resource Pathway Commons to act as a convenient access point for the pathway data represented in BioPAX and collected from many public databases, simplifying search visualization
and download of this data. This tutorial will help participants understand how to use the BioPAX ontology the expansive Pathway Commons dataset in their research projects, focusing on q-bio applications and make use of This tutorial will cover several topics: 1) a basic understanding of the BioPAX ontology, 2) the controlled vocabulary used as identifiers for entities created from the ontology, 3) an introduction to Paxtools, a Java-based programming interface for BioPAX, 4) accessing the Pathway Commons web service, 5)Mapping BioPAX to quantitative models and 6)visualization of BioPAX data.
