Course coordinators: Marco Roos, Katy Wolstencroft

: 30 November – 4 December 2015 
Location: SURF, Utrecht, the Netherlands
Registration: .Please not that this course is free of charge for PhDs who are or will become a member of the  BioSB research school, and with a reduced fee for other researchers who are or will  become a member of BioSB. More information about the BioSB membership can be found here: .
Course flyer

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

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).

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

 Marco Roos, Katy Wolstencroft, Frank van Harmelen, Paul Groth, Simon Jupp, Jesse van Dam, and others TBC

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
11:00-11:15 Coffee/Tea
11:15-12:30 An introduction to Linked Data
12:30-13:00 Lunch
13:00-15:00 Introduction to creating RDF and using a triple store (hands on session)
15:00-15:30 Surf Sara 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
10:45-11:00 Coffee/Tea
11:00-12:30 SPARQL hands-on session
12:30-13:30 Lunch
13:30-14:30 An Introduction the the EBI RDF platform and Ontologies
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
10:30-10:45 Coffee/Tea
10:45-12:30 Openphacts hands on session
12:30-13:30 Lunch
13:30-14:30 Guidelines and best practices for Linked Data
14:30-16:30 Hands on session
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
10:30-10:45 Coffee/Tea
10:40-12:30 Using tools for annotating and describing data – hands on session
12:30-13:30 Lunch
13:30-14:30 Ontologies in depth
14:30-16:30 Ontology hands-on
16:30-17:00 Wrap-up

Friday 04/12 – Using, Integrating and Analysing Data

09:30-10:30 An introduction to scientific workflows and distributed analyses
11:00-12:30 Designing and executing Taverna Workflows, hands-on
12:30-13:30 Lunch
13:30-15:00 Hands-on: Data integration with linked data (BYOD wrap up)
15:00-15:30 BYOD reports
15:30-16:15 The added value of FAIR data – Closing keynote
16:15-16:45 Wrap-up

Event date: 
Monday, November 30, 2015 - 13:45 to Friday, December 4, 2015 - 13:45