Ondex: data integration and visualisation for the Semantic Web Catherine Canevet 1 , Andrea Splendiani 1 , Steve Kuo 1,3 , Robert Stevens 2 , Phil Lord 3 , Chris Rawlings 1 1 Centre for Mathematical and Computational Biology, Rothamsted Research, Harpenden, UK 2 School of Computer Science, University of Manchester, Manchester, UK 3 School of Computing Science, University of Newcastle, Newcastle, UK Many systems approaches to biology need to identify, integrate and analyse information that is captured in a myriad of databases which use a wide variety of different formats and access methods. The Ondex data integration platform [1] (www.ondex.org) enables data from diverse biological data sets to be linked together, integrated, analysed and visualised using graph-based techniques. At the basis of Ondex is a graph data structure where entities and properties are associated to classes [2]. This data structure is closely related to the data model of RDF and supports a limited representation of ontologies. In the context of the SABR project (http://www.ondex.org/sabr.html), we are investigating ways to create a mapping between the Ondex data structure and the RDF/OWL. Our objective is to allow Ondex to query, visualise and analyse Semantic Web based knowledge bases [3]. The challenges are to maintain acceptable performance when translating between the RDF and Ondex data models. Once this mapping is implemented, Ondex could also be used to build workflows for the curation and management of such knowledge bases. The Ondex data model shares many similarities with RDF. For example, it has equivalents for Object Properties, Data Type properties, Types and Named graphs. On the other hand, one of the differences is that there are no global identities such as URIs available in Ondex. In fact, different information sources are aggregated by representing the original entities in “blank nodes” first and then by computing mappings among these nodes using their attributes. We wish to devise a mapping strategy that will allow Semantic Web based knowledge bases to be exposed using the Ondex data model because of the rich feature set that Ondex supports. Among the features already implemented in Ondex that could be deployed on a generic Semantic Web based knowledge bases are: ‐ Support for the definition of workflows using an Ondex-specific engine, via Taverna or a scripting interface