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Stardog is an insanely fast, commercial RDF database: SPARQL for queries; OWL for reasoning; pure Java for the Enterprise.

OWLIM is a family of semantic repositories, or RDF database management systems, with the following characteristics: native RDF engines, implemented in Java delivering full performance through both Sesame and Jena robust support for the semantics of RDFS, OWL 2 RL and OWL

"Wandora is a general purpose information extraction, management and publishing application based on Topic Maps and Java. Topic maps are hypergraphs with an emphasis on subjects. Wandora stores information in layered and auto-merging topic maps. Wandora has graphical user interface, multiple visualization models, huge collection of information extraction, import and export options, embedded HTTP server with several output modules and open plug-in architecture. Wandora is a FOSS application with GNU GPL license. Wandora suits well for constructing and maintaining vocabularies, ontologies and information mashups. "

RDF Gravity is a tool for visualising RDF/OWL Graphs/ ontologies.

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Cytoscape is an open source software platform for visualizing complex-networks and integrating these with any type of attribute data. A lot of plugins are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web.