Section: New Software and Platforms

AskOmics

Keywords: RDF - SPARQL - Querying - Graph - LOD - Linked open data

Functional Description: AskOmics allows to load heterogeneous bioinformatics data (formatted as tabular files) into a Triple Store system using a user-friendly web interface. AskOmics also provides an intuitive graph-based user interface supporting the creation of complex queries that currently require hours of manual searches across tens of spreadsheet files. The elements of interest selected in the graph are then automatically converted into a SPARQL query that is executed on the users' data.

News Of The Year: Several functionalities have been developed: 1) capacity of integrating genomics data (import of GFF and BED files and generation of RDF compliant with the FALDO ontology), 2) integration of data and knowledge in the OWL format to exploit biological information from external repositories, particularly from EBI and NCBI. Notably, this functionality allows AskOmics to support the Gene Ontology, the Taxonomy ontology as well as BioPAX biological networks. 3) improved user interface expressivity for generating SPARQL queries, 4) implementation of a support for multiple concurrent user sessions, with the distcintion between public and user-specific datasets 5) deployment of AskOmics on the GenOuest cloud infrastructure to facilitate its release and diffusion 6) interoperability between AskOmics and the Galaxy workflow environment.

• Authors: Charles Bettembourg, Xavier Garnier, Anthony Bretaudeau, Fabrice Legeai, Olivier Dameron, Olivier Filangi and Yvanne Chaussin

• Partners: Université de Rennes 1 - CNRS - INRA

• Contact: Fabrice Legeai

• URL: https://github.com/askomics/askomics