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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. A full list of features is reporte in Features.

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.

RDFScape is released as LGPL. Follow the link to Releases to download it . It is intended for users knowledgeable with ontologies and semantic web, but analysis procedures can be saved in databanks for a more generic public.

RDFScape depends on the following software and libraries:

  • The Systems Biology analysis and visualization software Cytoscape
  • The RDF / Semantic web library Jena
  • The OWL reasoner Pellet

For a description of version requirements refer to Dependencies


This project is primarily funded by Leaf Bioscience s.r.l. as an activity in the context of the EU DC-THERA Network of Excellence.

The conception and initial development of this project took place at the Systems Biology Unit of the Institut Pasteur and was partially funded by ESF.

For more informations mail andrea.splendiani -> dot net.

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