Exploring BioPax and the Pathway Commons API Using Linked Views

June 10th, 2015

Categories: Applications, Visualization, Visual Analytics, Visual Informatics

Screenshot of linked-view visualization approach.
Screenshot of linked-view visualization approach.


PhD candidate Paul Murray presents his research in biological data visualization techniques.

The Pathway Commons web service brings together several large biological databases, with tens of thousands of biological entities and interactions that can be traversed and queried through the Pathway Commons API. Query results are returned using the BioPax format (which is an RDF/XML OWL file), and each BioPax file contains a number of different relationship types. Rather than try to encompass a wide variety of node types and link types into a single visualization, a linked-view visualization approach is employed that presents each type of relationship in its own view, with linked interactions between views. This system is being integrated with the Pathway Commons API to enable effective visual queries of complex biological data.