The European Centre for Ontological Research – Future Perspectives in Biomedical Ontologies

AUTHORS: Brochhausen M 1, 2*

INSTITUTIONS: 1 European Centre for Ontological Research, Saarland University, Saarbrücken, Germany, 
2 Institute for Formal Ontology and Medical Information Science, Saarland University, Germany

BACKGROUND: Ontology development and ontological engineering are burgeoning knowledge management fields. As key paradigms of research in the domain of biomedical data management, they are put to use in a great number of ways. There is, however, a wide variety of so-called “ontologies,” and the candidates differ considerably with respect to the amount of knowledge they include (1). The European Centre for Ontological Research (ECOR) aims, as a consequence, to develop and advance common standards and techniques to be used in ontology development and ontological engineering.

OBJECTIVE: The Objective is to present the work of ECOR and to demonstrate how its work can influence ontology-based data management in the biomedical field.

METHODS: ECOR is a consortium of member and partner institutes working in the field of ontology development and ontological engineering. The idea behind ECOR is to bring together know-how from different institutions working in the field. Thus ECOR aims at providing joint resources on foundational aspects in ontology development, as well as guiding applications to different domains of data and knowledge management.
ECOR promotes a new approach to applying ontology to a variety of problems in information science and related areas (2). The core idea behind the ECOR initiative is to overcome concept-based knowledge management endeavours by advocating reality-based ontology development as the basis of ontological engineering. The biomedical field is one such domain that has seen numerous ontologies and/or terminologies attempting to tackle the diversity of biological and clinical reality, most of which failed to one degree or another (3). There are, nevertheless, a number of well-built ontologies in current use or under development in this field (4, 5). ECOR can act as an entity whose job is to consult and review efforts in biomedical ontology development, and check for theoretical consistency (which is a central feature of the work coordinated within ECOR (2)).

PERSPECTIVE: ECOR consists of nine member and four partner institutions, and amasses a broad knowledge basis on topics in ontological engineering. Some members of ECOR have already made notable contributions to biomedical ontologies. ECOR, we maintain, represents the optimal partner for the task of ensuring best practice in ontology development. Besides consulting, reviewing and developing ontologies, the certification of independently developed ontologies is also being contemplated as a future venue of activity for ECOR.

REFERENCES:

1. Lassila O,McGuinness DL. The Role of Frame-Based Representation on the Semantic Web. Knowledge Systems Laboratory Report KSL-01-02, Stanford University, 2001. 
2. http://www.ecor.uni-saarland.de/home.html
3. Ceuster W, Smith B, Kumar A, Dhaen C. Mistakes in Medical Ontologies: Where Do They Come From and How Can They Be Detected? In: Pisanelli DM (ed.): Ontologies in Medicine: Proceedings of the Workshop on Medical Ontologies, Rome, October 2003. IOS Press, Amsterdam, 2003.
4. Rosse C, Mejino JLV. A Reference Ontology for Bioinformatics: The Foundational Model of Anatomy. Journal of Biomedical Informatics 36:pp. 478-500, 2003.
5. Tsiknakis M, Brochhausen M, Nabrzyski J, Pucaski L, Potamias G, Desmedt C, Kafetzopoulos D. A semantic grid infrastructure enabling integrated access and analysis of multilevel biomedical data in support of post-genomic clinical trials on Cancer. IEEE Transactions on Information Technology in Biomedicine, (Special issue on Bio-Grids), in press.