Managing Life Science InformationNBIC course for Bioinformatics PhD students

(and others)

http://www.nbic.nl/biowise/school/EduProg/InfoMan09/ http://tinyurl.com/BioWiseInformationManagement

2

Factfile

• 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, 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.

3

What are key aspects for the Management of Life Science Information?

• BioAssistants say…– Security– Data compatibility– Data versioning– Data– Information life cycle management– Dissemination of data to other scientists– Transport and size– Data provenance– Usability– Searchability– Life science– Tools– Management

4

Research cycle

5

Data flow

6

Knowledge flow

7

Motivation

• Life science information is– about Life Science

• meaningless without interpretation– complex

• Biology is complex– scattered

• Many experiments with limited scope– often dead and buried in

'data graveyards‘• >1000 databases: ‘cottage industry’

8

Course credo

Keep your information alive

Or how to make your information understandable and computable

9

Day 1 and 2 – information and knowledge

• Knowledge-based information management– learn about how the Semantic Web

languages and tools can be used to manage biological data

– learn what OWL and RDF mean and why they exist

– acquire hands-on experience with these languages and tools

– learn about sharing knowledge and community-based science

10

Day 3 – processing information at large

• Database workhorses – 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/mySQL and MolGenis

11

Day 4 - Taverna and web services

• Taverna and web services for collaborative data integration – get a full tutorial on applying Taverna to

implement data integration pipelines– get hands-on experience with Taverna

12

Day 5 -  Hands-on Semantic Data integration

• Hands-on Semantic Data integration – deploy what you have learned on your

own application or on an example case, with experts present

13

What should the lecturers address?

• BioAssistants say…– Organisational issues– Reuse

• Including reuse storage facilities– Types of usage of data/information

• When to use what?– Who is doing what?– Web2.0– Reproducibility

• Example myExperiment

• Provenance• Social aspects

14

What cases would you like to address in the hands-on sessions?

• BioAssistants say…– …

Managing Life Science InformationNBIC course for Bioinformatics PhD students

(and others)

http://www.nbic.nl/biowise/school/EduProg/InfoMan09/ http://tinyurl.com/BioWiseInformationManagement