NBIC PhD Course on Managing and Integrating Life Science Information (3rd edition)

Course coordinators: Marco Roos, Katy Wolstencroft

Date: 17-21 June 2013
Location: Leiden University Medical Center, Leiden, the Netherlands
Website:
http://www.nbic.nl/education/nbic-phd-school/nbic-phd-school-course-portfolio/managing-and-integrating-information-in-the-life-sciences/
Registration:
http://www.nbic.nl/education/nbic-phd-school/enrolment/
Contact info: Celia van Gelder (
education@nbic.nl)

Target audience

This course is for bioinformaticians who would like to learn about leading-edge
data and knowledge integration solutions. You will learn (1) powerful and flexible
approaches to data and information management for your bioinformatics
application (Semantic web and Linked Data), (2) how to work with data across
remote locations, for instance by applying Web Services and workflows, (3) how to
publish your own data to get the most credit and make it available and reusable for
the rest of the community.

Description
The amount of Life Science data available in the public domain is a vast and
growing resource for bioinformatics research. There are over 20 million papers in
PubMed and over 1600 biological databases. In many cases finding and applying the
information from these resources is far from trivial. This course introduces modern techniques
for the management of life science data and knowledge for bioinformatics applications.
After following this course students should be able to start creating their first applications based
 on these technologies or make more informed design decisions for their current application.

In this course you will learn:

1.     how the 'Linked Data' principle works and how it can be applied for 'meaningful' data integration.

2.     how to expose your local data with rich metadata for use in other systems.

3.     how Web Services and workflows can be used to analyse distributed data.

4.     how to make publishable artefacts from your data for which you can get scientific credit.



Lecturers:

 Paul Groth (VU), Frank van Harmelen (VU), Marco Roos (LUMC), Egon
Willighagen (UM), Katy Wolstencroft (VU, University of Manchester)
.
Programme

Day 1: Introductions to Data integration

·         An introduction to the latest techniques in data and knowledge management

·         A semantic web primer

·         Hands on: A practical introduction to the semantic web - RDF and querying RDF

Day 2: Data to understandable data (generating and sharing data for reuse)

 

·         An introduction to minimum information models, identifiers and data standards

·         Hands on: A practical introduction data standards with RightField and Bioportal

·         RDF and dataset guidelines 

 

Day 3: Data to understandable data, part 2 (publishing and sharing)

 

·         An introduction to Nanopublications - a new way of publishing your data and results

·         Hands On: Creating and using Nanopublications

·          

Day 4: Integrating and using data (part 1)

 

·         An introduction to workflows and distributed

·         Hands on: A practical introduction to using the Taverna workbench

·         An introduction to Research Objects - describing the how and why of your experiments

 

Day 5: Integrating and using data (part 2)

 

·         An Introduction to provenance - recording the how and why of your experiments

·         The OpenPhacts project: using the Semantic Web for large-scale research projects

·         Hands on: Exploring OpenPhacts data



 

 

--

Dr. Celia W.G. van Gelder

Coordinator Education CMBI

Projectleader Education NBIC

tel. +31-(0)24-3666120

e-mail: C.vanGelder@cmbi.ru.nl

websites: www.cmbi.ru.nl, www.nbic.nl

 

Postal address:

CMBI 260

Radboud University Nijmegen-Medical Centre /NCMLS

PO Box 9101, 6500 HB Nijmegen

The Netherlands

 

 

 

-- 
Dr. Celia W.G. van Gelder
Coordinator Education CMBI
Projectleader Education NBIC
tel. +31-(0)24-3666120
e-mail: C.vanGelder@cmbi.ru.nl 
websites: www.cmbi.ru.nl, www.nbic.nl

Postal address:
CMBI 260
Radboud University Nijmegen-Medical Centre /NCMLS
PO Box 9101, 6500 HB Nijmegen
The Netherlands