General

Querying SIB Swiss Institute of Bioinformatics resources with SPARQL

SWAT4HCLS - Edinburgh (Dec. 2019)

The SIB Swiss Institute of Bioinformatics has been publishing data using Resource Description Framework (RDF) since 2007, with the UniProt knowledgebase as the first SIB resource to provide its data on the semantic web. Since then, more and more SIB resources are modelling their knowledge with RDF and made them queryable and accessible through their own SPARQL endpoints.

In this tutorial, we explain how you can use the data from nine independent SIB resources (GlyConnect, UniProt, Rhea, OrthoDB, OMA, Bgee, HAMAP, MetaNetX and neXtProt) to answer interesting biological questions.

For each resource, we present an introduction about what kind of data is available, followed by how it is modelled and then how you can query it using SPARQL. Then we illustrate the strength of SPARQL 1.1 federated queries to show how the connected SIB databases can answer more than any of our databases could independently.

Domain knowledge wise it covers proteins, glycans, reactions of biological interest, orthology, metabolic networks, chemical mapping, and genome/proteome annotations.

The tutorial starts with a quick introduction to RDF and SPARQL 1.1 in general.

At the end of the course, participants are expected to be able to:

• Have a basic understanding on SIB resources
  
• Have some understanding on RDF and SPARQL

Authors