David Bourget (Western Ontario)
David Chalmers (ANU, NYU)
Rafael De Clercq
Jack Alan Reynolds
Learn more about PhilPapers
Applied Ontology 5 (3):139-188 (2010)
Since 2002 we have been testing and reﬁning a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing speciﬁcally on our recommendation that ontologies developed for scientiﬁc purposes should be constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill’s critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative.
|Keywords||No keywords specified (fix it)|
|Categories||categorize this paper)|
Setup an account with your affiliations in order to access resources via your University's proxy server
Configure custom proxy (use this if your affiliation does not provide a proxy)
|Through your library|
References found in this work BETA
No references found.
Citations of this work BETA
Gary H. Merrill (2011). Ontology, Ontologies, and Science. Topoi (1):71-83.
Sabina Leonelli (2013). Classificatory Theory in Biology. Biological Theory 7 (4):338-345.
Similar books and articles
Gary H. Merrill (2010). Realism and Reference Ontologies: Considerations, Reflections, and Problems. Applied Ontology 5 (3-4):189-221.
Barry Smith, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Werner Ceusters, Louis J. Goldberg, Karen Eilbeck, Amelia Ireland, Mungall Christopher J., Neocles Leontis & et al (2007). The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration. Nature Biotechnology 25 (11):1251-1255.
Gary H. Merrill (2010). Ontological Realism: Methodology or Misdirection? Applied Ontology 5 (2):79-108.
Werner Ceusters & Barry Smith (2006). A Realism-Based Approach to the Evolution of Biomedical Ontologies. In Proceedings of the Annual AMIA Symposium. AMIA.
Barry Smith, Werner Ceusters, Bert Klagges, Jacob Köhler, Anand Kuma, Jane Lomax, Chris Mungall, , Fabian Neuhaus, Alan Rector & Cornelius Rosse (2005). Relations in Biomedical Ontologies. Genome Biology 6 (5):R46.
Cornelius Rosse, Anand Kumar, Jose L. V. Mejino, Daniel L. Cook, Landon T. Detwiler & Barry Smith (2005). A Strategy for Improving and Integrating Biomedical Ontologies. In Proceedings of the Annual Symposium of the American Medical Informatics Association. AMIA.
Anand Kumar & Barry Smith (2003). The Unified Medical Language System and the Gene Ontology: Some Critical Reflections. In KI 2003: Advances in Artificial Intelligence.
Barry Smith & Pierre Grenon (2004). The Cornucopia of Formal-Ontological Relations. Dialectica 58 (3):279–296.
Janna Hastings, Werner Ceusters, Mark Jensen, Kevin Mulligan & Barry Smith (2012). Representing Mental Functioning: Ontologies for Mental Health and Disease. In Towards an Ontology of Mental Functioning (ICBO Workshop), Proceeedings of the Third International Conference on Biomedical Ontology.
Pompeu Casanovas, Núria Casellas, Christoph Tempich, Denny Vrandečić & Richard Benjamins (2007). OPJK and DILIGENT: Ontology Modeling in a Distributed Environment. [REVIEW] Artificial Intelligence and Law 15 (2):171-186.
Barbara Heller & Heinrich Herre (2004). Ontological Categories in GOL. Axiomathes 14 (1-3):57-76.
Kenneth Bausch (2002). New Methods for Streamlining Theory Building. World Futures 58 (2 & 3):229 – 240.
Helen de Cruz & Johan de Smedt (2007). The Role of Intuitive Ontologies in Scientific Understanding – the Case of Human Evolution. Biology and Philosophy 22 (3):351-368.
Added to index2010-12-22
Total downloads17 ( #91,956 of 1,096,449 )
Recent downloads (6 months)3 ( #87,121 of 1,096,449 )
How can I increase my downloads?