Managing life science information

PhD course Managing life science information

Target audience: Bioinformatics PhD students
Lecturers: Ammar Benabdelkader, Peter Boncz, Andrew Gibson, Frank van Harmelen, Iwan Herman, M. Scott Marshall, Barend Mons, Marco Roos, Morris Swertz
Guest lectures: Carole Goble, Katy Wolstencroft
Coordinators: M. Scott Marshall, Marco Roos
Date: 25-29 May 2009
Location: Informatics Institute, F0.09, Science Park Amsterdam, the Netherlands
Limitations: For participants without their own laptop with wifi we have limited hands-on facilities.
Lecture points: 3EC (3 weeks)

Motivation

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 are known. However, a large number of information resources end up on an already formidable 'data graveyard'. Following this course can help you prevent your data or your information management system to have the same fate.

Target audience

If you would like to learn about how to perform powerful and flexible data and information management for your bioinformatics application, and how to work with data in distributed databases or through Web Services and workflows, or how a Web2.0 approach can help you reach out to users and leverage their contribution, then this course is for you. We assume a basic understanding of (relational) databases and programming.

Course description

This course introduces modern techniques for the management of life science data and knowledge for bioinformatics applications. Students will gain insight into Semantic Web languages and tools, federated databases, (Taverna) workflows, and Web2.0. 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.

Programme

Overview

Day 1 and 2 - Knowledge-based information management
- Where you will
  - learn about how the Semantic Web languages and tools can be used to manage biological data 'intelligently'
  - acquire some hands-on experience with these languages and tools
  - know what OWL and RDF mean and why they exist
  - learn about community-based science
Day 3 - Database workhorses
- Where you will
  - learn about how to use relational databases for managing heterogeneous and distributed data
  - learn how laboratory information can be realistically managed, example: MolGenis
  - get hands-on experience with postgreSQL and MolGenis
Day 4 - Taverna and web services for collaborative data integration
- Where you will
  - get a full tutorial on applying Taverna to implement data integration pipelines
  - get hands-on experience with Taverna
Day 5 - Hands-on Semantic Data integration
- Where you will deploy what you have learned on your own application or on an example case, with experts present
Day 5 + two weeks - Practical assignment
- Where you will work on a case to enjoy your new skills at information management (more details follow)
- We will celebrate your skills during a mini-symposium and drinks at the very end of the course

Agenda

Monday (F0.09)
- 9.00 Reception
- 9.30 Welcome by Scott Marshall and Marco Roos
- 10.30 Break
- 11.00 Why Semantic Web for e-bioScience? by Frank van Harmelen
- 12.30 Lunch
- 13.30 Managing distributed data by Ammar Benabdelkader
- 15.00 Break
- 15.30 A million minds to manage life science information .pptx by Barend Mons
- 17.00 Welcome Reception (Drinks!)
Tuesday (F0.09)
- 9.00 Introduction to Semantic Web languages and tools by Ivan Herman
- 10.30 Break
- 11.00 Introduction to Semantic Web languages and tools (cont.) by Ivan Herman
- 12.30 Lunch
- 13.30 Creating biological ontologies for applications by Andrew Gibson
- 15.00 Coffee & Tea
- 15.30 Semantic Web hands-on session
Wednesday (F0.09/e-BioLab)
- 9.30 'Practical laboratory information management' by Morris Swertz (F0.09)
- 10.30 Break
- 11.00 Querying XML-based resources by Peter Boncz (F0.09)
- 12.30 Lunch
- 13.30 'Practical laboratory information management' by Morris Swertz (e-BioLab)
- 15.00 Coffee & Tea
- 15.30 Hands on with MolGenis by Morris Swertz (e-BioLab)
- XX.XX 'Managing distributed data (cont.)' by Ammar Benabdelkader (e-BioLab, tentative)

Thursday (e-BioLab)
- 9.00 'Introduction to Taverna' by Katy Wolstencroft
- 10.30 Coffee and tea
- 11.00 'Taverna tutorial' by Katy Wolstencroft
- 12.30 Lunch
- 13.30 Hands on with Taverna
- 15.00 Coffee and Tea
- 15.30 Hands on with Taverna cont.
Friday (e-BioLab/F0.09)
- 9.00 'Health Care and Life Science interest group of W3C: Applications and Practice' by M. Scott Marshall (e-BioLab)
- Hands-on with experts (e-BioLab)
- 12.30 Lunch + Hands-on continued (e-BioLab)
- 13.30 'The Seven Sins of Bioinformtics' by Carole Goble (F0.09)
- 15.00 Discussion and wrap-up (F0.09)
- 16.00 Two-week practical assignments, closure, and drinks (F0.09)
Friday June 12 - Minisymposium Information management in Life Science (F0.09 - tentative)

Digital support

For collecting and sharing results of the hands-on sessions students are requested to sign up to myExperiment.org and join the BioWiseInformationManagement2009 group. Students and lecturers are member of the Google group BioWiseInformationManagement2009 for sharing documents, in particular for the two-week assignment following the week of lectures. (Follow the links to sign up and view the groups.)

Recommended Software

We would appreciate it if you could bring your own laptop. The software that we will use in the course includes:

Protégé 4

PostgreSQL

MolGenis

Taverna1.7.1 NB Look out for Taverna 2.1beta on the same site; it is close to being released.

e-DBI

SWObjects enables federation of SPARQL (also to SQL)

Please consider installing these software tools. If applicable also bring an example of a database you are working on so you can use it in the hands-on sessions (e.g. wrap your MySQL database using MOLGENIS). Don't worry if you have any trouble installing; we will help especially with software that is critical for the course.