Tutorial C
Pathway Commons and BioPAX
Monday October 12, 2015, 14:30 – 17:30 (1^st edition)
Tuesday October 13, 2015, 14:30 – 17:30 (2^nd edition)

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. A related resource Pathway Commons acts 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 and the expansive Pathway Commons dataset in their research projects, focusing on network applications. It 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) using BioPAX networks for data analysis,
6) visualization of BioPAX data.

Emek Demir got his Master of Science in Molecular Biology and Genetics at Bilkent University, Ankara, Turkey, in 2001. In 2005, he got his Ph.D. on Computer Science at the same University. Since then, he is working at the Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, USA, as Research Fellow and, since 2008, as Manager of the Pathway Information Resource.

His primary goal is to catalyze the construction of cell maps—formal, cell-scale, biochemical models of cellular processes—and use them to develop personalized medicine solutions. Cell maps cover and link a broad spectrum of cellular processes, including metabolism, signaling, and gene regulation, enabling computational reasoning over hundreds or even thousands of processes. Building cell maps is a multifaceted challenge that requires large-scale collaboration, computational tools as well as advancements in knowledge representation, visualization, and data integration.