Abstract

AskOmics is a web application for data integration and querying using the Semantic Web technologies. It helps users to convert multiple data sources (CSV/TSV files, GFF and BED annotation) into "RDF triples" and store them in a specific kind of database: an "RDF triplestore". Under this form, data can then be queried using a specific language: "SPARQL". AskOmics hides the complexity of these technologies and allows to perform complex queries using a user-friendly interface.

About This Material

This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.

Questions this will address

• How to integrate RNA-Seq results with other datasets using AskOmics?
• How to query these datasets to answer a biological question?
• How to exploit a distant SPARQL endpoint to retrieve information?

Learning Objectives

• Launch an AskOmics Interactive Tool
• Integrate RNA-Seq and reference datasets into AskOmics
• Create a complex query to get over-expressed genes, their location on the reference genome, and check if they are included in a known QTL
• Complete the query to get the human homologs and their location using neXtProt database