Topic outline

  • 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

    • Course material