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Martijn P. van Iersel, Joanna L. Parmley (General Bioinformatics Limited, Reading, UK)
We present a Cytoscape app to visualise data from the Semantic Web. More and more bioinformatics resources are now being made available as public SPARQL endpoints, such as Bio2RDF, the EBI RDF platform, and many others that are all pieces of the Semantic Web. Using federated queries it is now possible to connect a wide range of data types, from proteins to pathways to assays to ontologies, attaining a higher level of bioinformatics data integration than was ever possible before. The General SPARQL app lets you navigate the semantic web using an extensible set of pre-defined queries. The intuitive interface lets you start from a single entity of interest (such as a protein) and expand the network, seamlessly switching from one data type to the next. The app is pre-configured to visualise public data from Reactome, Uniprot, HGNC, NCBI Taxonomy, Chembl and more. The app is an open source contribution from General Bioinformatics Ltd. It is available from the Cytoscape app store, and can be made to work with any public or private RDF resource.