Workshop Overview
This workshop introduced several widely used ontologies for the life sciences. It familiarized participants with approaches to using these ontologies for data curation and integration. The content covered 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 presented use cases to illustrate both proven and experimental approaches to annotating biomedical data by combining existing ontologies on an 'as needs' basis. The workshop combined presentations, discussions and hands-on experience of using established approaches, encouraging participants to consider how to resolve common data sharing and integration problems within the BioMedBridges project. All partificpants contributed towards the creation of a 'living document' on ontologies to facilitate ongoing work throughout the BioMedBridges project.
Ontology Resources
The following pages contain useful information taken from the Living Document
Programme
| Time | Topic | Speaker |
|---|---|---|
| Day 1 - 4 March 2013 | ||
| 09:30 | Welcome and introduction | Tom Hancocks, BioMedBridges |
| 10:00 | Introduction to ontologies in the life sciences | Robert Stevens, University of Manchester |
| 10:30 | Break | |
| 11:00 | Current ontology landscape | Robert Stevens, University of Manchester & James Malone, EMBL-EBI |
| 12:00 | Participant slides | Robert Stevens, University of Manchester & James Malone, EMBL-EBI |
| 12:30 | Lunch | |
| 13:30 | Technology overview | Simon Jupp & James Malone, EMBL-EBI |
| 15:00 | Break | |
| 15:30 | Discussion session: delegate requirements | Tom Hancocks, BioMedBridges |
| 18:30 | Workshop Dinner | |
| Day 2 - 5 March 2013 | ||
| 09:30 | BMB use cases overview: * ArrayExpress and EFO * KupKB * Ontology use by the IMPC |
James Malone, EMBL-EBI Simon Jupp, EMBL-EBI /Robert Stevens, University of Manchester Terry Meehan, EMBL-EBI |
| 11:00 | Break | |
| 11:30 | BMB use cases overview: * Use of Ontologies in Instruct/PiMS * Systems microscopy; EuBi cellular phenotype ontology |
Chris Morris, STFC Gabriella Rustici, EMBL-EBI |
| 12:30 | Lunch | |
| 13:30 | The role of RDF and the semantic web | James Malone, EMBL-EBI |
| 15:00 | Break | |
| 15:30 | Discussion session: FAQ development | Tom Hancocks, BioMedBridges |
| 17:00 | Wrap up and evaluation | Tom Hancocks, BioMedBridges |
| 17:30 | End of workshop | |
Living Document
The Living Document created during the course can be viewed as a Google Doc: Practical Solutions with Ontologies
Slides
The slides used as part of the workshop have been uploaded onto this webpage for reference.
