Retrieving Pathway Data for Use in Kinetic Modeling

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Retrieving Pathway Data for Use in Kinetic Modeling

Oliver Ruebenacker

Center for Cell Analysis and Modeling

University of Connecticut Health Center

Purpose: We will provide theoretical background and hands-on experience on how to handle pathway data and use it to build and annotate reaction network models. To accomplish this, we will use the SyBiL, the Systems Biology Linker (, the Semantic Web tool of the Virtual Cell ( The theory will include an introduction into Semantic Web technology and ontologies.

Background: Pathway databases store enormous amounts of data usefull for building and annotating models: For example, the data of eight major pathway databases can be queried and exported through Pathways Common (, giving access to more than 418,000 interactions among 85,000 physical entities participating in 1,300 pathways. However, differences in the ways the pathway community and the modeling community approach questions of data representation disable a one-to-one map and require a sophisticated approach. A robust and flexible way for converting and linking data across communities is based on the use of a bridging ontology such as the Systems Biological Pathway Exchange (SBPAX).

The aims:

  1. To provide an introduction to the building and using ontologies.
  2. To describe popular ontologies used by biological communities such as: (a) Gene Ontology (GO, ), providing a controlled vocabulary to describe gene and gene product attributes; (b) Systems Biology Ontology (SBO,, and (c) BioPAX ontology ( designed to serves as a data exchange format for biological pathway data.
  3. To describe pathway databases that can serve as the source of data for modelers, such as Reactome ( ), Pathway Interaction Database (, and some others. Specifically, we will cover the ways to retrieve data, visualization modes, and supported data formats.
  4. To present obstacles to one-to-one mapping between BioPAX and the Systems Biology Markup Language (SBML,, a popular standard for cellular models.
  5. To give hands-on experience with retrieving pathway data from databases, visualizing it, and building and annotating models using the Systems Biology Linker (SyBiL,

Tutorial material: The course material consists of websites and of software that can be freely downloaded and installed in advance, such as the VCell ( and SyBiL (


  1. M. L. Blinov, O. Ruebenacker and I. I. Moraru (2008) Complexity and Modularity of Intracellular Networks – A Systematic Approach for Modeling and Simulation. IET Systems Biology, 2(5), 363-368.
  2. O. Ruebenacker, I. I. Moraru, J. C. Schaff and M. L. Blinov (2007) Kinetic Modeling Using BioPAX Ontology. Proceedings of the 2007 IEEE International Conference on Bioinformatics and Biomedicine: 339-348.
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