Hi,
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).
best, 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 CHU de Pontchaillou 2, rue Henri Le Guilloux 35033 Rennes - France Tel : +33 2 99 28 92 45 / +33 2 99 28 42 15 (secr.) Fax : +33 2 99 28 41 60 48° 07.275N 1° 41.643W
