Bioqueries: a collaborative environment to create, explore and share SPARQL queries in Life Sciences

María Jesús García-Godoy, Esteban López-Camacho, Ismael Navas-Delgado, José F. Aldana-Montes Bioqueries as a collaborative environment Bioqueries: a collaborative environment to create, explore and share SPARQL queries in Life Sciences Introduction Universidad de Málaga http://khaos.uma.es Features •Tools to create, clone test and execute SPARQL queries. •Complementary software tools like a visualization tool to preview the data structure of the endpoint to make easier the construction of new queries. •The retrieved information can be downloaded in formats such as RDF and N3 (N-triples) •Visualization of query results Acknowledgments Linked Data (http://linkeddata.org/) technology has emerged as a set of good practices based on the W3C’s specifications whose main goal is to publish data in standards formats like RDF (Resource Description Framework). RDF Databases are accessible by means of SPARQL queries. Bioqueries aims to bring either biologists or bioinformaticians closer to this emerging technology by accessing to this information. Bioqueries provides a collaborative environment to create,explore,execute,clone and share SPARQL queries (including Federated Queries). Federated SPARQL queries can retrieve information from more than one data source. María J. García Godoy, Esteban López-Camacho, Ismael Navas-Delgado, and José F. Aldana-Montes. Sharing and executing linked data queries in a collaborative environment. Bioinformatics, 29(13):1663-1670, July 2013 Bioqueries was initially populated with a seed of 100 SPARQL queries. Since then, Bioqueries has grown up to 373 SPARQL queries (59 federated queries) which have been classified into different groups according to manual annotations. Bioqueries’ evolution Reference http://bioqueries.uma.es/ http://sparql.es/ Queries are Classified in Categories Queries for a Database can be directly accessed Navigation is freely accessible Queries are manually validated Authors are acknowledged Users can read the documentation of a query Users can explore the SPARQL query (helping learning this language) User can introduce values for the query parameters, and execute the it Registration is optional, but only registered users can post new queries Results can be shown in different formats 250 users have registered in Bioqueries and have collaborated to create new SPARQL queries. In the last years, we also implemented new functionalities to improve Bioqueries. Some of these improvements are manual curation to validate queries, improved administration support and additional formats to download the query results. María J. García Godoy: [email protected] Esteban López-Camacho: [email protected] Ismael Navas-Delgado: [email protected] José F. Aldana-Montes: [email protected] Contact Details