In Carola Eschenbach & Michael Grüninger (eds.), Formal Ontology in Information Systems. IOS Press. pp. 21-35 (2008)
Increasingly, in data-intensive areas of the life sciences, experimental results are being described in algorithmically useful ways with the help of ontologies. Such ontologies are authored and maintained by scientists to support the retrieval, integration and analysis of their data. The proposition to be defended here is that ontologies of this type – the Gene Ontology (GO) being the most conspicuous example – are a part of science. Initial evidence for the truth of this proposition (which some will find self-evident) is the increasing recognition of the importance of empirically-based methods of evaluation to the ontology development work being undertaken in support of scientific research. Ontologies created by scientists must, of course, be associated with implementations satisfying the requirements of software engineering. But the ontologies are not themselves engineering artifacts, and to conceive them as such brings grievous consequences. Rather, ontologies such as the GO are in different respects comparable to scientific theories, to scientific databases, and to scientific journal publications. Such a view implies a new conception of what is involved in the authoring, maintenance and application of ontologies in scientific contexts, and therewith also a new approach to the evaluation of ontologies and to the training of ontologists.
|Keywords||applied ontology data standards peer review Gene Ontology|
|Categories||categorize this paper)|
References found in this work BETA
No references found.
Citations of this work BETA
Similar books and articles
Ontologies of Professional Legal Knowledge as the Basis for Intelligent IT Support for Judges.V. R. Benjamins, J. Contreras, P. Casanovas, M. Ayuso, M. Becue, L. Lemus & C. Urios - 2004 - Artificial Intelligence and Law 12 (4):359-378.
Framework for a Protein Ontology.Darren A. Natale, Cecilia N. Arighi, Winona Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, Barry Smith & Cathy H. Wu - 2007 - BMC Bioinformatics, Nov. 2007, 8(Suppl. 9) 8 (9):S1.
The Role of Intuitive Ontologies in Scientific Understanding – the Case of Human Evolution.Helen de Cruz & Johan de Smedt - 2007 - Biology and Philosophy 22 (3):351-368.
Realism and Reference Ontologies: Considerations, Reflections, and Problems.Gary H. Merrill - 2010 - Applied Ontology 5 (3-4):189-221.
Normalizing Medical Ontologies Using Basic Formal Ontology.Thomas Bittner & Barry Smith - 2004 - In Proceedings of GMDS 2004.
The Unified Medical Language System and the Gene Ontology: Some Critical Reflections.Anand Kumar & Barry Smith - 2003 - In KI 2003: Advances in Artificial Intelligence.
Beyond Concepts: Ontology as Reality Representation.Barry Smith - 2004 - In Formal Ontology in Information Systems (FOIS).
Added to index2009-01-28
Total downloads86 ( #61,350 of 2,177,981 )
Recent downloads (6 months)33 ( #8,198 of 2,177,981 )
How can I increase my downloads?