Teaching Good Biomedical Ontology Design

In Ronald Cornet & Robert Stevens (eds.), International Conference for Biomedical Ontologies (ICBO 2012), KR-MED Series, Graz, Austria July 21-25, 2012 (2012)
  Copy   BIBTEX

Abstract

Background: In order to improve ontology quality, tool- and language-related tutorials are not sufficient. Care must be taken to provide optimized curricula for teaching the representational language in the context of a semantically rich upper level ontology. The constraints provided by rigid top and upper level models assure that the ontologies built are not only logically consistent but also adequately represent the domain of discourse and align to explicitly outlined ontological principles. Finally such a curriculum must take into account the pre-existing skills and knowledge of the target audience. Objective: To develop a well-structured curriculum aligned to the particular requirements of life science professionals, in order to enable them to create logically sound, domain adequate and predicable ontologies using the Web Ontology Language (OWL) in Protégè. Methods: Content selection for the curriculum was based on the literature, pre-existing tutorials, and a guideline for good ontology development (i.e ontology design enhancing domain adequacy, sustainability and interoperability) that drew on the authors previous experiences with large ontology development projects. Learning objectives were formulated according to a needs assessment of the targeted learners, who were students trained in life sciences with basic knowledge and practical skills in computer science. As instructional format we choose an approach with a high amount of practical exercises. The curriculum was first implemented with 24 Students and 7 lecturers/ tutors over 5 full days. The curriculum was evaluated by gathering the participants feedback via a questionnaire. Results: Curricular development produced 16 modules of approximately 2 hours each, which covered basic principles of Applied Ontology, description logic syntax and semantics, as well as best design practices outlined in ontology design patterns and variants of the BioTop upper ontology. An opinion survey based on questionnaires indicated that the participants took advantage from the teaching strategies applied, as they indicated good knowledge gain and acknowledged the relevance of the modules. The difficulty was rated slightly lower. Conclusion: The development of teaching material for principled ontology design and best practices is of crucial importance in order to enhance the quality of biomedical ontologies. Here, we present a curriculum for a week long workshop, leveraging on current educational principles, focusing on interactive hands-on exercises, group interactions, and problem-oriented learning. Whereas evaluation clearly showed the success of this approach, in particular regarding student’s satisfaction, the objective measurement of traceable effects on the quality of the generated ontology, although of much higher interest, has just started.

Links

PhilArchive



    Upload a copy of this work     Papers currently archived: 90,616

External links

Setup an account with your affiliations in order to access resources via your University's proxy server

Through your library

Similar books and articles

Definition und Evaluation einer Guideline zur Entwicklung von qualitativ guten Ontologien.M. Boeker, S. Schulz, D. Seddig-Raufie, D. Schober, J. Röhl, N. Grewe & L. Jansen - 2013 - GMDS 2013: 58. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie Und Epidemiologie E.V. (GMDS). Lübeck 1.
Finding the Meaning in Images: Annotation and Image Markup.Daniel L. Rubin - 2011 - Philosophy, Psychiatry, and Psychology 18 (4):311-318.
A realism-based approach to the evolution of biomedical ontologies.Barry Smith - 2006 - In Proceedings of the Annual AMIA Symposium. Washington, DC: American Medical Informatics Association. pp. 121-125.

Analytics

Added to PP
2013-12-04

Downloads
31 (#445,254)

6 months
1 (#1,040,386)

Historical graph of downloads
How can I increase my downloads?

Author's Profile

Ludger Jansen
PTH Brixen College