Using Semantic Web for faster (Bio-)Research - November 2015
Topic outline
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Using the Semantic Web for faster (Bio-)Research
Geneva, 30 November - 3 December 2015
Trainers: Jerven Bolleman, SIB / Swiss-Prot
Marco Brandizi, EMBL-EBI
Frédéric Bastian, SIB / Evolutionary Bioinformatics
Kieron Taylor, EMBL-EBI
Mark Wilkinson, CBGP
Raoul Bonnal, INGM
Erik Garrison, Sanger Centre
Núria Queralt Rosinach, Pompeu Fabra University
Axel Ngonga, Universität Leipzig
Andrea Splendani, NovartisRuben Verborgh, Ghent University – iMinds
Daniel Teixeira, SIB /CALIPHO & SIB Technology
Venue: Classroom S1-2, CMU, University of Geneva ECTS: No Fee: Free for Staromics students. Others, please contact us Application deadline: 20 November 2015 Application status: closed Overview
Accessing and using existing public data is a hassle, yet it is crucial for designing good experiments. This 4 day course, co-organized by SIB and CUSO/Staromics, will teach PhD students on how to use semantic web technologies for their own research.
It includes an in-depth exploration of Semantic Web concepts such as RDF (data modelling), SPARQL (asking questions on your data), OWL (reasoning for deducing new facts about your data)The course will teach you how to use these technologies in your day to day research, as well as how you can share your data with the rest of the world.
The course will also include:- Modeling data tips and tricks
- Using the UniProt sparql endpoint for maximum efficiency
- Managing experimental results
- How to deploy SPARQL based software in a secure and efficient manner.
- How can you use OWL reasoning with RDF to test different hypothesis
- Linking programs with data, combining webservices with SPARQL via OWL
- Using BioRuby tools with SPARQL and RDF data
- Small and BigData better when combined
Learning objectives
At the end of the course, you should be able to:
- Work effectively with your own and other groups data using standardized technologies
- Understand when SPARQL and RDF are useful tools for your work
- Use the UniProt, neXtProt and among others the EBI RDF platform
Application is closed
Additional information
Coordination: Corinne Dentan, Grégoire Rossier
For administrative questions, please contact staromics@cuso.ch
For technical and scientific questions, please contact training@isb-sib.ch -
Day 1 Monday CMU S1/S2 November 30th 09:00 10:30 RDF What, when, why? Jerven Bolleman Coffee 10:45 12:00 Modeling experimental data for analysis and distribution Jerven Bolleman Lunch 13:00 14:30 SPARQL introduction and UniProt RDF&SPARQL: how to use Jerven Bolleman Coffee 14:45 17:00 EBI RDF platform: what is it, what does it contain Marco Brandizi Day 2 Tuesday CMU S1/S2 December 1st 09:00 10:15 DisGenet RDF&SPARQL: how to use + modeling challenges Núria Queralt Rosinach Coffee 10:30 11:45 Bgee, Uberon and an introduction to OWL Frederic Bastian Lunch 12:45 14:00 Genome Variation Graphs and their representation in RDF Erik Garrison 14:00 15:15 Client side SPARQL and Linked Data Ruben Verborgh Coffee 15:30 17:00 DBPedia and the life sciences Axel Ngonga Day 3 Wednesday CMU S2/S2 December 2nd 09:00 10:15 Ensembl RDF&SPARQL: how to use Kieron Taylor Coffee 10:30 11:45 SPARQL over programs, and workflows without effort using SADI Mark Wilkinson Lunch 12:45 14:00 BioRuby & Ruby-RDF Raoul Bonnal 14:00 15:15 Visualising SPARQL&RDF Daniel Teixeira Coffee 15:30 17:00 SemWeb at Novartis Andrea Splendani Day 4 Thursday Campus Biotech Geneva SIB Offices December 3rd 09:00 17:00 Hackathon - Bring your own data + Laptop
- Open to anyone (participants and teachers first, then anyone else)
- The idea here is to build rough prototypes that people can work out into production quality code afterwards.