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
| Jerven Bolleman | Introduction to RDF & SPARQL Glyconnect UniProt HAMAP EBI RDF Ensembl (Elixir friend) DisGeNET (Elixir friend) |
| Dmitry Kuznetsov | OrthoDB |
| Thierry Lombardot | Rhea IDSM (Elixir friend) |
| Julien Mariethoz | Glyconnect |
| Tarcisio Mendes de Faria |
Bgee OMA browser |
| Anne Morgat | Rhea IDSM (Elixir friend) |
| Marco Pagni | MetaNetX |
| Monique Zahn | neXtProt |
The views expressed in this information product are those of the author(s) and do not necessarily reflect the views of the SIB Swiss Institute of Bioinformatics