Biomedical Ontology. Philosophical Aspects of Health and Disease
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| Spear A, "Chapter 5: Introduction to Basic Formal Ontology and Relations. In: Spear A, Ontology for the Twenty First Century: An Introduction with Recommendations, 2006, Saarbrücken, p. 37-98. | Spear A, "Chapter 5: Introduction to Basic Formal Ontology and Relations. In: Spear A, Ontology for the Twenty First Century: An Introduction with Recommendations, 2006, Saarbrücken, p. 37-98. | ||
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| Available from: http://www.ifomis.org/bfo/documents/manual.pdf | Available from: http://www.ifomis.org/bfo/documents/manual.pdf | ||
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| Additional reading: | Additional reading: | ||
Revision as of 08:10, 21 August 2010
Monday, 4:00-6:00 pm, 141 Park. For more detail go here: http://www.philosophy.buffalo.edu/documents/Fall2010PHIGRADCourseDescriptionsApril9.pdf
Course Description
The focus of this course is the question: What is a disease? Topics to be addressed will include: the special problems of mental disease; what is it to be biologically normal?; the ontology of pain and other symptoms; the role of genes and environment. We shall also address more general ontological problems in biology, including: What is a species? What is a biological function? Preliminary reading: Neil Williams, The Factory Model of Disease, http://goliath.ecnext.com/coms2/gi_0199-8835041/The-factory-model-of-disease.html PHI
Reading Assignment by M. Brochhausen
On relations in (bio)medicine:
Gupta et al "Towards a formalization of disease-specific ontologies for neuroinformatics." Neural Networks 16 (2003) 1277–1292.
Available from: http://www.bioontology.org/wiki/images/7/75/Gupta_disease_ontology.pdf
Smith B, Grenon P “The Cornucopia of Formal-Ontological Relations”, Dialectica 58: 3 (2004), 279–296.
Available from: http://ontology.buffalo.edu/smith/articles/cornucopia.pdf
Davidson D: The Logical Form of Action Sentences (1967) [plus Criticism, Comment, and Defence]. In: Davidson D: Essays on Action and Events. Second Edition, 2001, Oxford, New York, p. 105-149.
Spear A, "Chapter 5: Introduction to Basic Formal Ontology and Relations. In: Spear A, Ontology for the Twenty First Century: An Introduction with Recommendations, 2006, Saarbrücken, p. 37-98.
Available from: http://www.ifomis.org/bfo/documents/manual.pdf
Additional reading:
Smith B, Ceusters W, Klagges B, Köhler J, Kumar A, Lomax J, Mungall C, Neuhaus F, Rector A, Rosse C “Relations in Biomedical Ontologies”, Genome Biology (2005), 6 (5), R46.
Available from: http://genomebiology.com/2005/6/5/R46
Ontological realism for the clinical world
Smith B, Brochhausen M (2008) Establishing and Harmonizing Ontologies in an Interdisciplinary Health Care and Clinical Research Environment.In: Blobel B, Pharow P, Nerlich M (eds.): eHealth: Combining Health Telematics, Telemedicine, Biomedical Engineering and Bioinformatics on the Edge. Global Expert Summit Textbook. (Health, Technology and Informatics, 134), IOS Press, Amsterdam, 219-234
Available from: http://ontology.buffalo.edu/medo/eHealth.pdf
Brochhausen M, Spear AD, Cocos C, Weiler G, Martìn L, Anguita A, Stenzhorn H, Daskalaki E, Schera F, Schwarz U, Sfakianakis S; Kiefer S, Dörr M, Graf N, Tsiknakis M (2010) The ACGT Master Ontology and Its Applications - Towards an Ontology-Driven Cancer Research and Management System. Journal of Biomedical Informatics. E-published ahead of print. DOI 10.1016/j.jbi.2010.04.008
Species as one example for process patterns in biology and biomedicine
Sterelny K, Griffiths PE: "Chapter 9: Species." In: Sterelny K, Griffiths PE: Sex and Death. An Introduction to Philosophy and Biology. 1999, Chicago, London, p.180-214.
