Semscape - Visualizing Semantic Data Landscapes with Cytoscape 3.0 (GSoC 2012)

Semscape is a cytoscape 3.0 plugin which was developed by Yigang Zhou in the Google Summer of Code 2012. The project was mentored by Andra Waagmeester, Andrea Splendiani, Helena Deus, and me. 
Semscape allows to explore RDF endpoints via SPARQL queries and graphically represents the results in Cytoscape. In contrast to existing RDF visualization solutions, Semscape not only can represent data extracted out of SPARQL endpoints, but also the underlying schema of the data. This feature makes it much easier to explore foreign endpoints, where the RDF model is unknown.

For more information see:

• Installation: https://code.google.com/p/vsdlc3/wiki/DownloadRunSetup 
• UserGuide: https://code.google.com/p/vsdlc3/wiki/UserGuide 
• Blog: http://vsdlc3.blogspot.de/

SIGINT 2012 - Raising of the Dead?

The slides of my talk "The Semantic Web - Raising of the Dead?" at SIGINT 2012 can be found here. Also the video of my talk is available here. An embedded version will hopefully follow soon.

Update: And here is a youtube version

How to generate Java files from OWL-files in Jena - Extension

This is an extension of Andra Waagmester's "How to generate Java files from OWL-files in Jena."

For some files, like the PAV OWL-file, you will just get the header, but none of the predicates or classes. Here is the reason why:

Schemagen is picking a namespace for your ontology, and is defaulting to the value of the xmlns-attribute:

<rdf:RDF xmlns="&pav;2.0/"
     xml:base="&pav;2.0/"

Hence http://purl.org/pav/2.0/

However, all of their declarations are actually in a non-versioned namespace:

xmlns:pav="http://purl.org/pav/"

So it is necessary to tell schemagen to use the right namespace with -a, or change the file so that the namespaces are consistent. Run:

java -cp lib/icu4j-3.4.4.jar:lib/jena-arq-2.9.0-incubating.jar:lib/jena-core-2.7.0-incubating.jar:lib/jena-iri-0.9.0-incubating.jar:lib/log4j-1.2.16.jar:lib/slf4j-api-1.6.4.jar:lib/slf4j-log4j12-1.6.4.jar:lib/xercesImpl-2.10.0.jar:lib/xml-apis-1.4.01.jar jena.schemagen -i $inputFile -o "./src" --package "de.fraunhofer.scai.bio.uima.xcas2rdf.vocabulary" --owl -a "http://purl.org/pav/" pav

.. and it will generate what is expected.

Another tip is to add  --ontology to get OntProperty, OntClass, etc, declarations generated in the output file.