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Managing Life Science Information

17-21 & 28 October 2011, Science Park, Amsterdam, the Netherlands.

Lecturers

Scott Marshall & Marco Roos

Confirmed guest lecturers

Andrew Gibson, Frank van Harmelen, Erik Roos, Kristina Hettne, Paul Groth, Katy Wolstencroft

Coordinators

M. Scott Marshall, Marco Roos

Location

Science Park Amsterdam, the Netherlands

Limitations

None, the lectures take place in a computer class room; a personal laptop may come in handy, but is not required.

Credits and grading

The total studyload of the course is 3 EC. There will not be a written examination. Participants will get a final assignment which will be discussed on Friday October 28.

Background

Considering the complexity of biological systems it is not surprising that the management of life science information is one of the most challenging aspects of bioinformatics. For example, (medical) biologists have compiled over 17 million papers, and well over a thousand databases. In many cases finding and applying the information from these resources is far from trivial. In fact, a majority ends up on a formidable 'data graveyard' (how many of the >1000 databases do you know?). Following this course can help you prevent your data or your information management system to follow the same fate.

Target audience

This course is for bioinformaticians who would like to learn about leading edge information management solutions, as well as traditional approaches. You will learn (1) powerful and flexible approaches to data and information management for your bioinformatics application, (2) how to work with data across remote locations, for instance by applying Web Services and workflows, (3) how a Web2.0 approach can help you reach out to users and leverage their contribution. We assume a basic understanding of (relational) databases and programming for the hands-on sessions.

Course description

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 how:

  1. the 'Linked Data' principle works and how it can be applied for 'meaningful' data integration.
  2. to expose your local data (in traditional databases) for use in other systems.
  3. Web Services can be used to analyse data from anywhere.
  4. text mining can be applied to link resources such as biobanks.
  5. human knowledge can be made computable and associated with data.
  6. to make your data publishable artefacts for which you can get scientific credit.
  7. tools work such as MolGenis, Taverna, SPARQL, D2R, SWobjects, NCBO's BioPortal, Anni, LarKC (Large Knowledge Collider).
  8. to collaboratively solve an information management problem.

Concept programme

Monday:

  • Introduction by leading Semantic Web expert (Frank van Harmelen)
  • Hands-on with RDF and SPARQL (Scott Marshall)

Tuesday:

  • XML, RDF, Minimal information models, and exposing data in local databases (Scott Marshall)
  • hands-on with MolGenis (Erik Roos)

Wednesday:

  • Data integration with Web Services (Katy Wolstencroft)
  • Hands-on with Taverna (Katy Wolstencroft)

Thursday:

  • Knowledge management and nano-publication (Andrew Gibson)
  • hands-on federated queries with SWObjects (Scott Marshall)

Friday:

  • Text mining for linking biobanks and hands-on with Anni (Erik Roos, Kristina Hettne)
  • Hands-on with LarKC (Paul Groth)
  • DRINKS!!!

Registration

See Enrolment Page.

More information

For more information about the course programme you can contact Marco Roos or Scott Marshall.
For more information about the registration or logistics you can contact Celia van Gelder.

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