Course: Managing and Integrating Life Science Information (4th edition): Approaches using Linked Data and Semantics


Next occasion: 2017 (5th edition) – you can pre-register here
Last occasion: November 30, 2015 – December 4, 2015

** Please note that the information below concerns the 2015 edition of the course! Updated information will follow. **

Course flyerflyer

Managing and Integrating Information in the Life Sciences_Course_2015


Marco Roos, Katy Wolstencroft, Frank van Harmelen, , Simon Jupp, Jesse van Dam, Andre Dekker, Ronald Siebes

Course Coordinators

Marco Roos and Katy Wolstencroft

Credits and grading

The total study load of the course is 3 EC. There will not be a written examination.


SURF, Utrecht, The Netherlands

Kantoren Hoog Overborch (Hoog Catharijne)
Moreelsepark 48
3511 EP Utrecht

Find route here
Google maps

Hosted by: SURFacademy



None. A computer will be provided for computer sessions, but a personal laptop would be an advantage.


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. Following this course will show you techniques for working with these distributed resources, which includes using the web of Linked data and scientific workflows. It will also focus on methods for using or linking your own data into this large distributed Semantic Web of resources, in order to ensure that your data is FAIR (Findable, Accessible, Interoperable and Reusable).

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 make it available and reusable for the rest of the community. We assume a basic understanding of bioinformatics programming for the hands on sessions. It would suit previous user participants of BYOD meetings who would like more hands-on experience of data integration. It would also suit data providers who would like to explore new ways of serving their data or integrating it with other resources.

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 about:

  1. Linked Data and the Semantic Web technologies that underpin it
  2. How you can use Linked Data for data and knowledge integration in the Life Sciences
  3. Available Linked Data resources in the public domain and large-scale projects that use these resources
  4. How you can integrate your own data with Linked Data resources
  5. How you can combine data integration and analysis over distributed resources, using Web Services and workflows

Tentative programme

Monday 30/11 – Introduction to Semantic Interoperability and the Semantic Web
09:00-09:30 Coffee/Tea
09:30-09:45 Introduction and workshop goals
09:45-11:00 Semantic Web Primer – Frank van Harmelen
11:00-11:15 Coffee/Tea
11:15-12:30 An introduction to Linked Data tutorial – Marco Roos
12:30-13:00 Lunch
13:00-15:00 Introduction to creating RDF and using a triple store (hands on session) – Marco Roos
15:00-15:30 SURFsara services for researchers
15:30-…….. Welcome drinks

Tuesday 01/12 – The Semantic Web in Use
09:30-10:00 Define course projects/interests (BYOD)
10:00-10:45 An Introduction to Constructing SPARQL Queries – Jesse van Dam
10:45-11:00 Coffee/Tea
11:00-12:30 SPARQL hands-on session – Jesse van Dam
12:30-13:30 Lunch
13:30-14:30 An Introduction to the EBI RDF platform and Ontologies – Simon Jupp
14:30-16:30 Querying the EBI RDF platform, hands-on

Wednesday 02/12 – The Semantic web in use – systems and guidelines
09:30-10:30 The OpenPHACTS project – Ronald Siebes
10:30-10:45 Coffee/Tea
10:45-12:30 Openphacts hands on session – Ronald Siebes
12:30-13:30 Lunch
13:30-14:30 An introduction to scientific workflows and distributed analyses – Katy Wolstencroft
14:30-16:30 Designing and executing Taverna Workflows, hands-on – Katy Wolstencroft
16:30-17:00 Wrap-up

Thursday 03/12 – Making Data Understandable and Searchable
09:30-10:30 An Introduction to Describing and Annotating Data: Case Study in systems Biology – Katy Wolstencroft
10:30-10:45 Coffee/Tea
10:40-12:30 Using tools for annotating and describing data – hands on session – Katy Wolstencroft
12:30-13:30 Lunch
13:30-16:30 Hands on session and Guidelines and best practices for linked data
16:30-17:00 Wrap-up

Friday 04/12 – Using, Integrating and Analysing Data
09:30-10:30 Ontologies in Depth – Marco Roos
10:30-10:45 Coffee/Tea
11:00-12:30 Hands-on: Data integration with linked data (BYOD)
12:30-13:30 Lunch
13:30-14:30 Hands-on: Data integration with linked data continued (BYOD)
14:30-15:30 BYOD reports
15:30-16:15 Closing keynote – Andre Decker
16:15-16:45 Wrap-up

More information

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