Towards unifying systems biology - using pathway data in BioPAX format for SBML simulators

Thousands of biochemical interactions are available in the Biological Pathways Exchange (BioPAX) format. However, BioPAX is structurally and semantically different from the current standard for exchange of simulation-ready biological models, Systems Biology Markup Language (SBML). To take full advantage of existing pathway data in kinetic modeling, a comprehensive modeling framework capable of representing the complex relationships between SBML and BioPAX data is needed. We describe such a framework that we are developing as a part of the VCell modeling and simulation environment. The platform for SBML-BioPAX integration is called Sybil (Systems Biology Linker), which is used to load and visualize BioPAX data, and which supports SBPAX (Systems Biology Pathway Exchange), an OWL/RDF-based language for gluing BioPAX data to SBML models. To consolidate and validate data, Sybil uses SYBREAM (Systems Biology Reasoning Engine for Analysis and Modeling) that is based on user-specified assumptions.

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-- OliverRuebenacker - 26 May 2008