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AskOmics is a web software for data integration and query using the Semantic Web technologies. It helps users to convert multiple data sources (CSV/TSV files, GFF and BED annotation) into RDF triples, and perform complex queries against this files, but also on distant SPARQL endpoint. AskOmics provide a user-frendly interface to build the queries so users don't have to learn the SPARQL language.
AskOmics comes useful for cross-referencing results datasets with various reference data. For example, in RNA-Seq studies, we often need to filter the results on the fold change and the p-value, to get the most significant deferentially expressed genes. These genes often need to be linked on the reference genome to obtain more information about their location. Then, we may need to determine if these genes are part of a QTL associated with a phenotype of interest. Finally, we can have access to distant endpoints to get disease linked to our genes, or publications.
AskOmics offers a solution to 1) automatically convert the multiple data formats to RDF and 2) use a user-friendly interface to perform complex SPARQL queries on the RDF datasets to find the genes you are interested in and 3) cross-reference local datasets with distant databases (NeXtProt for example).
During this training session, we will use the Galaxy AskOmics Interactive Tool to integrate galaxy datasets into an AskOmics instance. Then we will perfom complex queries against this data and a distant SPARQL endpoint
NeXtProt to answer a biological questions.
Prerequisites- Basic knowledge about RNA-seq
- A laptop with a modern web browser. Google Chrome, Firefox and Safari will work best
