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Announcing RDFScape: Cytoscape plugin to read and reason on ontologies

From: Andrea Splendiani <andrea.splendiani@univ-rennes1.fr>
Date: Fri, 8 Feb 2008 10:38:26 +0100
Message-Id: <17AFAFEC-29D9-4724-9FB6-72A2172A522A@univ-rennes1.fr>
To: public-semweb-lifesci@w3.org


I would like to announce the availability of RDFScape[1] (v0.4) a  
software that makes it possible to read, query, browse and visualize  
RDF/OWL ontologies within the popular systems biology software  
Cytoscape [2].

Unlike other ontology related features of Cytoscape, RDFScape treats  
ontology through a reasoner, where both standard entailments  
(OWL,RDF... with a choice of Jena reasoners or Pellet) and custom  
inference rules can be computed.

This means original ontologies can be "interpreted" within cytoscape.  
For instance, a biopax representation of pathways in humans (say from  
PathwayCommons/Reactome) can be abstracted and visualized as an  
interaction network, or as a cause-effect network (once a concept of  
cause-effect is defined through axioms).

Apart from this, it offers query possibility within Cytoscape (SPARQL  
and others) and a nice visualization tool for ontologies. It also  
offers an interactive ontology browsing function (the rdf network can  
be interactively expanded) and the possibility to define query as  
graph patterns (visually).

Andrea Splendiani

[1] http://www.bioinformatics.org/rdfscape/
[2] http://www.cytoscape.org

Andrea Splendiani
post-doc, bootstrep project (www.bootstrep.eu)

UPRES-EA 3888 - Laboratoire d'Informatique Médicale
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Received on Friday, 8 February 2008 09:39:06 UTC

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