RDFScape is a project that brings Semantic Web "features" to the popular Systems Biology software Cytoscape. It allows to query, visualize and reason on ontologies represented in OWL or RDF within Cytoscape.
Unlike other ontology-based features in Cytoscape, RDFScape doesn't consider ontologies as annotation, but as a knowledge-base that can be interpreted through standard inference processes and through custom inference rules. The result is that ontologies can be interpreted for specific analysis needs. For instance, a pathway ontology such as biopax can be easily abstracted to an interaction network. Or as a causal network, once of notion on causal effect is defined on the ontology.
Beside this, RDFScape offers reach query capabilities on ontologies (SPARQL, RDQL, Strings, interactive browsing) and a customizable visualization features.
Current version of RDFScape is 0.4.1 and offers a rich set of features to query, visualize and overlay ontologies on other Cytoscape networks. Future versions of RDFScape will address the interpretation of experimental data given ontological a-priori information.