Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format

For the purpose of converting biochemical interactions into the BioPAX format, which is the leading standard developed by the computational systems biology community, we developed an open-source command line tool that takes as input tabular data describing different types of molecular biochemical interactions. The tool converts such interactions into the BioPAX level 3 OWL format. We used the tool to convert several existing and new mammalian networks of protein interactions, signalling pathways, and transcriptional regulatory networks into BioPAX. Some of these networks were deposited into PathwayCommons, a repository for consolidating and organizing biochemical networks.The software tool Sig2BioPAX is a resource that enables experimental and computational systems biologists to contribute their identified networks and pathways of molecular interactions for integration and reuse with the rest of the research community.BioPAX is a protocol for the specification and representation of cell signaling pathways, gene-regulatory networks, protein-protein interactions and other types of biomolecular interaction data [1]. There are several software tools that use the BioPAX format for pathway visualization and analysis for hypotheses generation. For example, the popular tool Cytoscape allows customizable visualization and easy navigation of different types of networks [2]. Cytoscape plug-ins, including the popular BiNGO [3], and other plugins such as BiNoM [4], and cPath [5] further extend Cytoscape's capabilities for pathway analysis, data visualization, and data integration. BiNGO is a plugin that statistically analyzes a set of genes and their corresponding Gene Ontology functional annotations to determine which functional categories are overrepresented in that gene set. BiNGO uses Cytoscape's visualization capabilities to display the results. BiNoM is a plugin that performs structural analysis of networks, identifying strongly connected components, paths and cycles. cPat