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The 2017 Galaxy Community Conference (GCC2017) is being held in Montpellier, France, 26-30 June.  GCC2017 will include keynotes and accepted talks, poster sessions, demos, birds-of-a-feather meetups, exhibitors, and plenty of networking opportunities. There will also be three days of pre-conference activities, including hackathons and training. If you work in data-intensive biomedical research, there is no better place than GCC2017 to present your work and to learn from others.
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Thursday, June 29 • 15:40 - 17:00
D01: Integration of Linked Data into Galaxy using AskOmics

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Xavier Garnier 1,2, Olivier Dameron 2, Olivier Filangi 1,3, Fabrice Legeai 1,4, Anthony Bretaudeau 1,3

1 : Institut de Génétique, Environnement et Protection des Plantes  (IGEPP), Institut National de la Recherche Agronomique : UMR1349, Universite de Rennes 1 : UMR1349, Agrocampus Ouest : UMR1349, Domaine de la Motte au Vicomte BP 3532735653 Le Rheu -  France
2 : DYLISS  (INRIA - IRISA)INRIA, Universite de Rennes 1, CNRS : UMR6074, Campus de Beaulieu 35042 Rennes cedex -  France
3 : Plateforme bio-informatique Genouest  (Genouest), genouestIRISA/INRIA Plateforme GenOuest Campus de Beaulieu 35042 Rennes cedex, France -  France
4 : GenScaleI, RISA/INRIA équipe Genscale Campus de Beaulieu 35042 Rennes cedex, France -  France

Experiments that produce large amounts of data are now routinely performed at the scale of a laboratory. Results of these experiments are stored into files or loaded into relational databases. However, analyzing these data typically requires to combine them with other data and knowledge bases.

Semantic Web technologies such as RDF and SPARQL are key elements for combining datasets, which has led to the emergence of linked data.

AskOmics (AGPL, https://github.com/askomics/) is a web application supporting both intuitive data integration and querying. It provides a user-friendly interface to hide the technical difficulties inherent to the use of RDF and SPARQL technologies.

AskOmics automatically integrates tabular or GFF files and generates the corresponding RDF triples. It also provides a visually intuitive graph-based querying interface. Complex queries are built by selecting a sequence of nodes in a graph, and defining data filters. The corresponding SPARQL query is generated by AskOmics and executed on the selected datasets.

In this demo we will present the integration of AskOmics with Galaxy: Galaxy tools to integrate data into a remote AskOmics server (using Askocli, AGPL, https://github.com/askomics/askocli), and AskOmics ability to retrieve datasets from Galaxy and export results into it (using BioBlend). This opens the door to an Interactive Environment currently under final development.
The compatibility of AskOmics with Galaxy allows users to connect their pipelines to AskOmics in a simple way and bridge the gap between Galaxy and the Semantic Web.

avatar for Xavier Garnier

Xavier Garnier

INRA, IGEPP and Dyliss Team
I am working on AskOmics, a web tool to integrate and query biological data using Semantic Web technologies, and its interaction with Galaxy

Thursday June 29, 2017 15:40 - 17:00
Le Corum Le Corum

Attendees (7)