Integration of Linked Data into Galaxy using Askomics

Xavier Garnier 1 Olivier Dameron 1 Olivier Filangi 2, 3 Fabrice Legeai 2, 4 Anthony Bretaudeau 2, 3
1 Dyliss - Dynamics, Logics and Inference for biological Systems and Sequences
Inria Rennes – Bretagne Atlantique , IRISA_D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
3 Plateforme bioinformatique GenOuest [Rennes]
UR1 - Université de Rennes 1, Plateforme Génomique Santé Biogenouest®, Inria Rennes – Bretagne Atlantique , IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires
4 GenScale - Scalable, Optimized and Parallel Algorithms for Genomics
Inria Rennes – Bretagne Atlantique , IRISA_D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
Abstract : 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.
Type de document :
Communication dans un congrès
Galaxy Community Conference, Jun 2017, Montpellier, France. 2017
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https://hal.inria.fr/hal-01576870
Contributeur : Fabrice Legeai <>
Soumis le : jeudi 24 août 2017 - 11:21:29
Dernière modification le : vendredi 16 novembre 2018 - 01:22:18

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  • HAL Id : hal-01576870, version 1

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Xavier Garnier, Olivier Dameron, Olivier Filangi, Fabrice Legeai, Anthony Bretaudeau. Integration of Linked Data into Galaxy using Askomics . Galaxy Community Conference, Jun 2017, Montpellier, France. 2017. 〈hal-01576870〉

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