Looking into Reactome through Biopax Lens

Abstract—In order to understand cell behavior under different conditions, the computational simulation of biological pathways is of great interest. Hence, to simulate a biological pathway computationally, extensive knowledge of protein-protein interactions (PPIs) in the pathway is required, along with the information about the generic flow of the pathway components i.e. biological reactions, which comprise the concerned pathway. The popularity of Semantic Web technologies in tackling the integrative bioinformatics challenges has increased, with various approaches used to aggregate and correlate data from different sources. However the integration of publicly available pathway databases, to determine the different PPIs and hence effectively simulate the cell behavior, has still various obstacles. In this paper, we present a semantic approach in pathway-wise analysis of protein-protein interactions (PPIs) using Biopax standards focusing particularly on Reactome database. We have identified the PPIs involved in a given pathway by the hierarchical extraction of its components (complexes, proteins, small molecules). We have developed a visualization tool which automatically generates a visual representation of the directed graph of PPIs in any specified pathway. Our approach provides intuitive inference of the data by flattening the nested pathways in Reactome and their components instead of wrapping each layer of data in the shell of outer pathway. We have also discussed that the representation of a pathway in Biopax standard format is highly complex and even contains redundant information. Hence tools are needed in order to facilitate the navigation and analysis of pathway datasets, which have been structured in Biopax format. I