BioMedBridges Knowledge Exchange Workshop: Practical Solutions with Ontologies
This workshop will introduce some of the most widely used ontologies for the life sciences. It will familiarize attendees with approaches to using these ontologies for data curation and integration. The content will cover the role of ontologies in the wider framework of interoperability, such as the semantic web framework and the use of RDF to describe data. BioMedBridges partners will present use cases to illustrate both proven and experimental approaches to annotating biomedical data by combining existing ontologies on an 'as needs' basis. The workshop will combine presentations, discussions and hands-on experience of using established approaches, to encourage participants to consider how to resolve common data sharing and integration problems within the BioMedBridges project. All delegates will contribute towards the creation of a 'living document' on ontologies to facilitate ongoing work throughout the BioMedBridges project.
Is it right for me?
No previous experience with ontologies is required to attend. The workshop is aimed at those interested in solutions for data integration, sharing and curation of data in the biomedical sciences, especially within the context of data produced and used by the emerging ESFRI biomedical science research infrastructures.
|Day 1 - 4 March 2013 (Materials from day 1)|
|09:30-10:00||Welcome and introduction||Tom Hancocks, BioMedBridges|
|10:00-10:30||Introduction to ontologies in the life sciences: what are they? How are they are structured? What do we use them for?||Robert Stevens, University of Manchester|
|11:00-12:00||Current ontology landscape – what's out there in the wide world, what sort ofthings do they cover, how are they used?||Robert Stevens, University of Manchester & James Malone, EMBL-EBI|
|12:00-12:30||One slide (no more than one) from each BMB member summarising what they’d like to describe, overview of data and sharing needs||Robert Stevens, University of Manchester & James Malone, EMBL-EBI|
|13:30-15:00||Technology overview – what languages are used, what tools help build and useontologies?||Simon Jupp & James Malone, EMBL-EBI|
|15:30-17:30||Discussion session: delegate requirements||Tom Hancocks, BioMedBridges|
|Day 2 - 5 March 2013 (Materials from day 2)|
|09:30-11:00||BMB use cases overview:
* ArrayExpress and EFO
* Ontology use by the IMPC
|James Malone, EMBL-EBI
Simon Jupp, EMBL-EBI /Robert Stevens, University of Manchester
Terry Meehan, EMBL-EBI
|11:30-12:30||BMB use cases overview:
* Use of Ontologies in Instruct/PiMS
* Systems microscopy; EuBi cellular phenotype ontology
|Chris Morris, STFC
Gabriella Rustici, EMBL-EBI
|13:30-15:00||Wider integration with other data – the role of RDF and the semantic web||James Malone, EMBL-EBI|
|15:30-17:00||Discussion session: FAQ development||Tom Hancocks, BioMedBridges|
|17:00-17:30||Wrap up and evaluation||Tom Hancocks, BioMedBridges|
|17:30||End of workshop|
Registration will be via a selection process therefore applicants should be aware that, in order to be considered for place on this course, you MUST complete the application page. Incomplete applications will NOT be considered.
Application registration closes 1 February 2013 (12:00 midday GMT). There will be a maximum of 25 participants on this course. Successful applicants will be notified by 8 February 2013 and will then be asked to confirm their place on the course by re-registering.
- Lunch and refreshment breaks for both days
- Workshop dinner on 4 March 2013
- Course materials
- Use of EBI IT Training Room computer during the 2 day course.
NOTE: All delegates will need to arrange and pay for their own travel to and from the course as well as accommodation. Accommodation can be arranged directly with the onsite accommodation Wellcome Trust Conference Centre.
Application is now closed
Please complete the application form through the link below. Items marked * are mandatory. Incomplete registrations will not be processed: