An ontology based query engine for querying biological sequences

Martijn Devisscher, Tim De Meyer, Wim Van Criekinge, Peter Dawyndt


This work presents the design and proof of principles of Boinq, a flexible query engine for querying and analysing sequence data based on bio-ontology based annotations.

The Boinq framework is a web application that allows querying sequencing data in a user friendly way. The application includes a genome browser, and a query builder component that builds SPARQL queries to interrogate endpoints providing sequence annotations.

It contains a visualization component for inspection of the data using a genome browser, and an interface for defining the analysis that needs to be done. The analysis will be split up in two steps: (1) Definition of a region of interest by combining a number of simple match operators, and (2) Definition of the analysis [still under construction]

The framework also offers a number of SPARQL endpoints that act as sources for delivering feature information as RDF data, and a SPARQL endpoint providing metadata about the feature datasources. These endpoints are queried by the framework, both to fetch the features, and to compose the queries for filtering these feature based on the match operators.


next generation sequencing; ontology; query engine

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