Managing Life Science Information
NBIC course for Bioinformatics PhD students
(and others)
http://www.nbic.nl/biowise/school/EduProg/InfoMan09/
http://tinyurl.com/BioWiseInformationManagement

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.
2

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
3

Research cycle
4

Data flow
5

Knowledge flow
6

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’
7

Course credo
Keep your information alive
Or how to make your information
understandable and computable
8

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
9

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
10

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
11

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
12

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
13

What cases would you like to address in the
hands-on sessions?
• BioAssistants say…
–…
14

Managing Life Science Information
NBIC course for Bioinformatics PhD students
(and others)
http://www.nbic.nl/biowise/school/EduProg/InfoMan09/
http://tinyurl.com/BioWiseInformationManagement