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