Practical introduction to SPARQL for biologists and informaticians

Overview

This workshop will be divided in three parts.

The first part is an introduction to SPARQL (approx 2 hours).
The second part will focus on using and creating SPARQL queries on the neXtProt SPARQL engine (www.nextprot.org). This part will explore how to create complex queries making the best use of the wealth of information available in neXtProt as well as taking advantage of federated queries across "remote" resources such as DrugBank, ChEMBL and PDB.
The third part focuses on the UniProt SPARQL engine (sparql.uniprot.org) introducing the UniProt data model and showing example queries.

Audience

Users interested in learning SPARQL and in developing queries for neXtProt and UniProt

Learning Objectives

At the end of the course you should have gained

Basic knowledge about RDF, SPARQL and its practical applications;
A basic understanding ot the neXtProt and UniProt RDF data models and how you can use SPARQL to get answers to complicated questions;
Some practical experience with the tools and help neXtProt and UniProt provide (example queries, data model browser).

Prerequisites

Knowledge / competencies:

To be familiar with UniProtKB and/or neXtProt is an advantage to better understand the use cases, but this is not mandatory
Limited experience with command line tools

Technical:

Personal laptop with WIFI/internet access is needed
Java 1.7 or higher installed on your laptop. You can check the Java version by opening a command line tools and typing: java -version. If you don’t have Java installed please follow this link: https://java.com/en/download/help/index_installing.xml

Application

The registration fees for academics are 50 CHF. This includes course content material and coffee breaks.Participants from non-academic institutions should contact us before application.

Please note that participation to SIB courses is subject to this and other general conditions, available at https://www.sib.swiss/training/terms-and-conditions

You will be informed by email of your registration confirmation.

Location

University of Lausanne, Genopode Building, room 2020

Additional information

You are welcome to register to the SIB courses mailing-list to be informed of all future courses and workshops, as well as all important deadlines using the form here.