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2013 Archived Content

 SC16 Ontologies for the Bio-Science Industry: Development & Use  

Monday, February 20, 2012 | 4:30 – 7:30 PM

C WernerCourse Instructor: Werner Ceusters, M.D., Professor, Department of Psychiatry; Director, Ontology Research Group, NYS Center of Excellence in Bioinformatics & Life Sciences

Dr. Ceusters is a neuro-psychiatrist with additional degrees in Knowledge Engineering, Informatics and business aspects of the bio-science industry. As Director of the Ontology Research Group of the New York State Center of Excellence in Bio-informatics and Life Sciences, he focuses his research on the development of realism-based ontologies and the use thereof in life science applications, specifically for the integration of data from heterogeneous resources. He is the major contributor to the ontology requirements specifications for the knowledge management infrastructure being build under Europe’s ‘Innovative Medicine’ program.

Course Overview:

There is a growing trend in the life sciences to move away from traditional terminology-based ontologies and to embrace instead the principles of Ontological Realism. These principles form the basis for the Open Biomedical Ontology (OBO) Foundry; their aim is the development of ontologies that are more stable and that are able to support automated reasoning using a semantics that is more powerful than semantic web languages. The same principles are embedded in Referent Tracking, which is a methodology not only to use OBO Foundry ontologies for the annotation of datasets in such a way that the data are rendered maximally reusable for other purposes than they have originally been collected, but also for the design of data collection protocols and dictionaries that minimize the problems related to ambiguities, missing data elements, and implicit assumptions.
 
The course is aimed at informatics practitioners in the biological sciences, and pharmaceutical and healthcare industries who are responsible for setting up and maintaining data resources covering multiple domains, and at information managers who seek to familiarize themselves with ontology driven data integration and analysis in healthcare and life sciences.

At the time of registration for the course but not later than 2 weeks before the event, attendees may submit questions and problems to the instructor which will be covered during the course.

Course Agenda:  

4:30 The problems of terminology-based ontologies
4:50 Principles of Ontological Realism
5:20 From model-theoretic languages to reference-based languages
5:50  Refreshment break
6:00 Overview of OBO Foundry ontologies

PRACTICAL EXAMPLES

6:20 Documenting adverse events
6:40 Integrating clinical datasets about orofacial pain
7:00 Q&A and addressing pre-submitted questions and problems.
7:30 Close of Course

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