Breakout session:

SPARQLing Biology; a beginners course (room 1+2)

Organizers:

• Denise Slenter, Maastricht University, BiGCaT bioinformatics group
• Egon Willighagen, Maastricht University, BiGCaT bioinformatics group
• Marvin Martens, Maastricht University, BiGCaT bioinformatics group

More biological databases are being offered in the so called Resource Description Framework (RDF) format, which is a flexible way of sharing data in a machine readable manner. SPARQL is a (semantic) query language for these databases, allowing to find information within the RDF data.

During this tutorial, the basics of RDF and SPARQL will be explained in a lecture. Later, a hands-on session is planned with some biological examples from the Wikidata SPARQL website.

Two key examples which will be discussed, are: "Which variant of which gene predicts a positive prognosis in colorectal cancer" and "Find drugs for cancers that target genes related to cell proliferation". These examples can be modified during the hands-on session, to allow for direct implementation for the field of interest of the participants.

After the hands-on session, we will demonstrate some examples on how the acquired knowledge can be translated to other life science databases.

For whom?

This tutorial will be at a basic level; therefore you do not need programming skills to work with SPARQL queries. Understanding which biological questions to ask is more important.