Towards Unifying Systems Biology - Using Pathway Data in Biopax Format for SBML Simulators

Abstract

Thousands of biochemical interactions are available from public sources in the Biological Pathways Exchange (BioPAX) format. However, the current standard for exchange of simulation-ready biological models is System Biology Markup Language (SBML). This markup language is structurally and semantically different from BioPAX. Some conversion schemes exist, using annotations and based on simple one-to-one mappings between SBML and BioPAX objects, which ignores semantic differences and therefore often leads to significant loss of information or meaning. A comprehensive modeling framework capable of representing the complex relationships between SBML and BioPAX data is needed to take full advantage of existing pathway data in kinetic modeling, thus integrating these two formats by gluing them together.Here we describe such a framework that we are developing as a part of the Virtual Cell (http://vcell.org) modeling and simulation environment. Systems Biology Linker (SyBiL, http://vcell.org/biopax) is a tool for analyzing and visualizing BioPAX data, and converting them to SBML. Based on the Jena Semantic Web framework for Java, SyBiL supports handling of generic RDF/OWL data (such as visualization and reasoning) as well as functions specific to handling SBML and BioPAX data. SyBiL uses Systems Biology Pathway eXchange, called SBPAX, as a generic approach to integrate model-centric formats similar to SBML with pathway-centric formats similar to BioPAX. SBPAX is an OWL-based schema that serves as a glue to integrate different data formats, despite semantic differences. Effectively, SBPAX provides a bridge between SBML and the Semantic Web world. SyBiL offers various visualization modes showing reaction networks to varying degrees of details, including displaying nodes for reactions only as well as displaying Petri nets consisting of reaction nodes and reaction participants and catalysts.