Ontology and Its Applications - Revision history

Phismith at 19:09, 13 March 2018

2018-03-13T19:09:12Z

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	== '''The Course''' ==		== '''The Course''' ==

	This course will provide an introduction to ontology at the beginning graduate-student level ~~with~~ a ~~focus on~~ applications in biomedical and social ~~ontology~~.		This course will provide an introduction to ontology and its applications at the beginning graduate-student level. We will describe the roots of contemporary ontology in classical metaphysics, explain how ontology now plays a role in data science and information fusion, and outline a series of applications of ontology in the biomedical and social sciences.

	Department of Philosophy: Special Topics PHI 598. Registration number:		Department of Philosophy: Special Topics PHI 598. Registration number: #####

	'''Time''': Monday, 1-3:50pm, Fall 2018		'''Time''': Monday, 1-3:50pm, Fall 2018

Phismith: /* October 15: Organisms and Environments */

2018-03-13T18:57:51Z

October 15: Organisms and Environments

← Older revision		Revision as of 18:57, 13 March 2018
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	*Biological Environments		*Biological Environments
	*Human Environments		*Human Environments
			*The Microbiome
	*Environments, Settings and Behavior		*Environments, Settings and Behavior
	:[http://ontology.buffalo.edu/smith/articles/napflion.pdf Objects and Their Environments: From Aristotle to Ecological Ontology]		:[http://ontology.buffalo.edu/smith/articles/napflion.pdf Objects and Their Environments: From Aristotle to Ecological Ontology]

Phismith at 15:26, 13 March 2018

2018-03-13T15:26:39Z

← Older revision		Revision as of 15:26, 13 March 2018
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	:See also materials [http://ncorwiki.buffalo.edu/index.php/Workshop_on_BFO_and_the_Ontology_of_Social_Entities_2016 here]		:See also materials [http://ncorwiki.buffalo.edu/index.php/Workshop_on_BFO_and_the_Ontology_of_Social_Entities_2016 here]

	~~== November 12 :~~		== November 19: == The Ontology of Organizations
	== November 19: ==

	== November 26: Presentations of Student Projects 1==		== November 26: Presentations of Student Projects 1==

Phismith at 15:03, 13 March 2018

2018-03-13T15:03:46Z

← Older revision		Revision as of 15:03, 13 March 2018
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	Introduction to the Ontology of Medicine		Introduction to the Ontology of Medicine

	== October 1: *Mental Health and Disease ==		== October 1: Mental Health and Disease ==

	== October 8: ~~How~~ to ~~Keep Track of Absolutely Everything~~ ==		== October 8: Introduction to Referent Tracking==
	~~Werner on Referent Tracking~~

	== October 15: ~~Document Acts~~==		== October 15: Organisms and Environments ==
	:[http://ontology.buffalo.edu/smith/articles/~~document-acts~~.pdf ~~Document Acts~~]		*Biological Environments
	:[http://~~college~~.~~holycross~~.~~edu~~/~~faculty~~/~~aborghin~~/~~Articles~~/~~Philosophy_of_Food~~/~~Borghini_2015_JAEE_WhatIsARecipe~~.pdf ~~What is a Recipe?~~]		*Human Environments
	:[http://ontology.buffalo.edu/smith/courses16/Analytic_Metaphysics/7.~~pptx~~ Slides]		*Environments, Settings and Behavior
	:[https://www.youtube.com/watch?v=~~DRZzYR6_jho~~ Video]		:[http://ontology.buffalo.edu/smith/articles/napflion.pdf Objects and Their Environments: From Aristotle to Ecological Ontology]

			== October 22: The Ontology of Experimentation, Classification and Measurement==
			:[http://hl7-watch.blogspot.com/2008/02/weight-of-baby.html The Weight of the Baby]
			:[http://hem.passagen.se/ijohansson/function1.pdf Functions, Function Concepts, and Scales]
			:[http://ontology.buffalo.edu/smith/courses16/Analytic_Metaphysics/9.ppt Slides]
			:[https://www.youtube.com/watch?v=D3Y5sfnvd5Y Video]

	Mind, Language, Intentionality, Emotions, Truth, and Aboutness ==		== October 29: Mind, Language, Intentionality, Emotions, Truth, and Aboutness ==
	:[http://ncor.buffalo.edu/2015/icbo-aboutness.pdf About Aboutness]		:[http://ncor.buffalo.edu/2015/icbo-aboutness.pdf About Aboutness]
	:[http://ontology.buffalo.edu/smith/articles/STIDS-2013.pdf Information Artifact Ontology]		:[http://ontology.buffalo.edu/smith/articles/STIDS-2013.pdf Information Artifact Ontology]
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	:[https://www.youtube.com/watch?v=PBKsupBquok&feature=youtu.be Video 2: About Aboutness]		:[https://www.youtube.com/watch?v=PBKsupBquok&feature=youtu.be Video 2: About Aboutness]

			== November 5: Document Acts==
			:[http://ontology.buffalo.edu/smith/articles/document-acts.pdf Document Acts]
			:[http://college.holycross.edu/faculty/aborghin/Articles/Philosophy_of_Food/Borghini_2015_JAEE_WhatIsARecipe.pdf What is a Recipe?]
			:[http://ontology.buffalo.edu/smith/courses16/Analytic_Metaphysics/7.pptx Slides]
			:[https://www.youtube.com/watch?v=DRZzYR6_jho Video]

			== November 12: Ontology of Deontic Entities ==
	== ~~October 22~~: Ontology of Deontic Entities ==
	:[https://mitpress.mit.edu/index.php?q=books/building-ontologies-basic-formal-ontology Building Ontologies with Basic Formal Ontology, Chapter 5]		:[https://mitpress.mit.edu/index.php?q=books/building-ontologies-basic-formal-ontology Building Ontologies with Basic Formal Ontology, Chapter 5]
	:[http://www.youtube.com/watch?v=AaFnMesr6uQ Massively Planned Social Agency]		:[http://www.youtube.com/watch?v=AaFnMesr6uQ Massively Planned Social Agency]
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	:[http://ontology.buffalo.edu/smith/articles/SearleIntro.pdf John Searle: From Speech Acts to Social Reality]		:[http://ontology.buffalo.edu/smith/articles/SearleIntro.pdf John Searle: From Speech Acts to Social Reality]
	:[http://ontology.buffalo.edu/smith/courses16/Analytic_Metaphysics/2.pdf Slides] [[Contents]]		:[http://ontology.buffalo.edu/smith/courses16/Analytic_Metaphysics/2.pdf Slides] [[Contents]]
	:[https://www.youtube.com/watch?v=W4Vefe5p6p4 Video]:[http://www.youtube.com/watch?v=AaFnMesr6uQ Massively Planned Social Agency]		:[https://www.youtube.com/watch?v=W4Vefe5p6p4 Video]
			:[http://www.youtube.com/watch?v=AaFnMesr6uQ Massively Planned Social Agency]
	:[http://ontology.buffalo.edu/smith/courses16/Analytic_Metaphysics/3.pdf Slides]		:[http://ontology.buffalo.edu/smith/courses16/Analytic_Metaphysics/3.pdf Slides]
	:[https://youtu.be/Hk6Df2geYiQ Video]		:[https://youtu.be/Hk6Df2geYiQ Video]
	:See also materials [http://ncorwiki.buffalo.edu/index.php/Workshop_on_BFO_and_the_Ontology_of_Social_Entities_2016 here]		:See also materials [http://ncorwiki.buffalo.edu/index.php/Workshop_on_BFO_and_the_Ontology_of_Social_Entities_2016 here]

	~~== October 29: The Ontology of Experimentation, Classification and Measurement==~~		== November 12 :

	~~:[http://hl7-watch.blogspot.com/2008/02/weight-of-baby.html The Weight of the Baby]~~
	~~:[http://hem.passagen.se/ijohansson/function1.pdf Functions, Function Concepts, and Scales]~~
	~~:[http://ontology.buffalo.edu/smith/courses16/Analytic_Metaphysics/9.ppt Slides]~~
	~~:[https://www.youtube.com/watch?v=D3Y5sfnvd5Y Video]~~

	~~== November 5: Organisms and Environments ==~~
	*Biological Environments
	*Human Environments
	*Environments, Settings and Behavior
	~~:[http://ontology.buffalo.edu/smith/articles/napflion.pdf Objects and Their Environments: From Aristotle to Ecological Ontology]~~

	== November 12: ~~Terrorism, Wars and Warfighting==~~

	~~:[http://www.sozphil.uni-leipzig.de/cm/philosophie/files/2013/01/2006b.pdf Defining Terrorism]~~
	~~:[http://www.casede.org/BibliotecaCasede/SOF_RoleCombatingTOC.pdf#page=157 An Ontological Framework for Understanding the Terror-Crime Nexus]~~
	~~:[http://militaryontology.com/ Military Ontology]~~
	~~:[http://ontology.buffalo.edu/smith/courses16/Analytic_Metaphysics/11.pdf Slides]~~
	~~:[https://www.youtube.com/watch?v=8MlxZtLnshQ Video]~~

	== November 19: ==		== November 19: ==

Phismith at 14:52, 13 March 2018

2018-03-13T14:52:39Z

← Older revision		Revision as of 14:52, 13 March 2018
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	Introduction to the Ontology of Medicine		Introduction to the Ontology of Medicine

	== October 1:		== October 1: *Mental Health and Disease ==
	*Mental Health and Disease=



	== October 8: How to Keep Track of Absolutely Everything ==		== October 8: How to Keep Track of Absolutely Everything ==

Phismith at 14:51, 13 March 2018

2018-03-13T14:51:01Z

← Older revision		Revision as of 14:51, 13 March 2018
Line 1:		Line 1:
	== '''The Course''' ==		== '''The Course''' ==

			This course will provide an introduction to ontology at the beginning graduate-student level with a focus on applications in biomedical and social ontology.
	This course will provide an introduction to ontology at the beginning graduate-student ~~label,~~ with a ~~discussion of~~ applications in ~~of central themes in~~ social ontology viewed from a broadly realist perspective. The course will be of interest not only to philosophers but also to those interested in ontological applications, including applications in biomedical informatics.

	Department of Philosophy: Special Topics PHI 598. Registration number:		Department of Philosophy: Special Topics PHI 598. Registration number:
Line 23:		Line 22:

	== August 27: Introduction to Ontology==		== August 27: Introduction to Ontology==
	~~Aristotle~~
	~~:[http://ontology.buffalo.edu/smith/articles/What'sWrong.pdf What's Wrong with Contemporary Philosophy?]~~
	~~:[http://ontology.buffalo.edu/smith/book/austrian_philosophy/ Austrian Philosophy]~~
	~~:[http://ontology.buffalo.edu/smith/articles/napflion.pdf Objects and Their Environments: From Aristotle to Ecological Ontology]~~
	~~:[http://ontology.buffalo.edu/smith/book/P&M/pieces.pdf Pieces of a Theory]~~
	:[http://ontology.buffalo.edu/smith/courses16/Analytic_Metaphysics/1.ppt Slides]		:[http://ontology.buffalo.edu/smith/courses16/Analytic_Metaphysics/1.ppt Slides]
	:[https://www.youtube.com/watch?v=9ZG0-71Qk6s Video]		:[https://www.youtube.com/watch?v=9ZG0-71Qk6s Video]
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	Introduction to the Ontology of Medicine		Introduction to the Ontology of Medicine

	== October 1: ~~Mind, Language, Intentionality, Emotions, Truth, and Aboutness ==~~		== October 1:
	~~:[http://ncor.buffalo.edu/2015/icbo-aboutness.pdf About Aboutness]~~
	~~:[http://ontology.buffalo.edu/smith/articles/STIDS-2013.pdf Information Artifact Ontology]~~
	~~:[http://ontology.buffalo.edu/smith/courses16/Analytic_Metaphysics/6.pptx Slides]~~
	~~:[https://www.youtube.com/watch?v=bnLE7-8bRHs Video 1]~~
	~~:[https://www.youtube.com/watch?v=PBKsupBquok&feature=youtu.be Video 2: About Aboutness]~~

	*Mental Health and Disease=		*Mental Health and Disease=

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	:[https://www.youtube.com/watch?v=DRZzYR6_jho Video]		:[https://www.youtube.com/watch?v=DRZzYR6_jho Video]

			Mind, Language, Intentionality, Emotions, Truth, and Aboutness ==
			:[http://ncor.buffalo.edu/2015/icbo-aboutness.pdf About Aboutness]
			:[http://ontology.buffalo.edu/smith/articles/STIDS-2013.pdf Information Artifact Ontology]
			:[http://ontology.buffalo.edu/smith/courses16/Analytic_Metaphysics/6.pptx Slides]
			:[https://www.youtube.com/watch?v=bnLE7-8bRHs Video 1]
			:[https://www.youtube.com/watch?v=PBKsupBquok&feature=youtu.be Video 2: About Aboutness]


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	*Human Environments		*Human Environments
	*Environments, Settings and Behavior		*Environments, Settings and Behavior
			:[http://ontology.buffalo.edu/smith/articles/napflion.pdf Objects and Their Environments: From Aristotle to Ecological Ontology]

	== November 12: Terrorism, Wars and Warfighting==		== November 12: Terrorism, Wars and Warfighting==

Phismith: Created page with "== '''The Course''' == This course will provide an introduction to ontology at the beginning graduate-student label, with a discussion of applications in of central themes i..."

2018-03-13T14:45:24Z

Created page with "== '''The Course''' == This course will provide an introduction to ontology at the beginning graduate-student label, with a discussion of applications in of central themes i..."

New page

== '''The Course''' ==

This course will provide an introduction to ontology at the beginning graduate-student label, with a discussion of applications in of central themes in social ontology viewed from a broadly realist perspective. The course will be of interest not only to philosophers but also to those interested in ontological applications, including applications in biomedical informatics.

Department of Philosophy: Special Topics PHI 598. Registration number:

'''Time''': Monday, 1-3:50pm, Fall 2018

'''Room''': 200G Baldy

'''Instructors''': [http://ontology.buffalo.edu/smith Barry Smith] and [http://www.referent-tracking.com/RTU/ceusters_vita.html Werner Ceusters]

'''Office hours''': By appointment via email to [mailto:phismith@buffalo.edu]

<div class="noautonum">__TOC__</div>

== '''Recommended background reading''' ==

:R. Arp, B. Smith, A. D. Spear, ''[https://mitpress.mit.edu/index.php?q=books/building-ontologies-basic-formal-ontology Building Ontologies with Basic Formal Ontology]''

== '''Schedule''' ==

== August 27: Introduction to Ontology==
Aristotle
:[http://ontology.buffalo.edu/smith/articles/What'sWrong.pdf What's Wrong with Contemporary Philosophy?]
:[http://ontology.buffalo.edu/smith/book/austrian_philosophy/ Austrian Philosophy]
:[http://ontology.buffalo.edu/smith/articles/napflion.pdf Objects and Their Environments: From Aristotle to Ecological Ontology]
:[http://ontology.buffalo.edu/smith/book/P&M/pieces.pdf Pieces of a Theory]
:[http://ontology.buffalo.edu/smith/courses16/Analytic_Metaphysics/1.ppt Slides]
:[https://www.youtube.com/watch?v=9ZG0-71Qk6s Video]

== September 10: Ontological Realism and Basic Formal Ontology ==
:[http://ontology.buffalo.edu/bfo/IUC.pdf Individuals, Universals and Collections]
:[http://ontology.buffalo.edu/smith/articles/fiat.htm Fiat Objects]
:[http://link.springer.com.gate.lib.buffalo.edu/article/10.1007%2Fs11098-010-9526-z Endurantist and Perdurantist Accounts of Persistence]
:[http://ontology.buffalo.edu/smith/courses16/Analytic_Metaphysics/4.pdf Slides]
:[https://www.youtube.com/watch?v=lcyKZKxFx5A Video]
*[http://ontology.buffalo.edu/bio/logic_of_classes.pdf The Logic of Biological Classification and the Foundations of Biomedical Ontology]
*[http://ontology.buffalo.edu/smith/articles/niches.pdf The niche]

== September 17: Functions, Capabilities, Dispositions ==

== September 24: Diseases, Disabilities, Diagnoses ==
Introduction to the Ontology of Medicine

== October 1: Mind, Language, Intentionality, Emotions, Truth, and Aboutness ==
:[http://ncor.buffalo.edu/2015/icbo-aboutness.pdf About Aboutness]
:[http://ontology.buffalo.edu/smith/articles/STIDS-2013.pdf Information Artifact Ontology]
:[http://ontology.buffalo.edu/smith/courses16/Analytic_Metaphysics/6.pptx Slides]
:[https://www.youtube.com/watch?v=bnLE7-8bRHs Video 1]
:[https://www.youtube.com/watch?v=PBKsupBquok&feature=youtu.be Video 2: About Aboutness]

*Mental Health and Disease=

== October 8: How to Keep Track of Absolutely Everything ==
Werner on Referent Tracking

== October 15: Document Acts==
:[http://ontology.buffalo.edu/smith/articles/document-acts.pdf Document Acts]
:[http://college.holycross.edu/faculty/aborghin/Articles/Philosophy_of_Food/Borghini_2015_JAEE_WhatIsARecipe.pdf What is a Recipe?]
:[http://ontology.buffalo.edu/smith/courses16/Analytic_Metaphysics/7.pptx Slides]
:[https://www.youtube.com/watch?v=DRZzYR6_jho Video]

== October 22: Ontology of Deontic Entities ==
:[https://mitpress.mit.edu/index.php?q=books/building-ontologies-basic-formal-ontology Building Ontologies with Basic Formal Ontology, Chapter 5]
:[http://www.youtube.com/watch?v=AaFnMesr6uQ Massively Planned Social Agency]
:[https://www.youtube.com/watch?v=JWN4Uo-GjjE Document Acts and the Ontology of Social Reality]
:[http://ontology.buffalo.edu/smith/articles/SearleIntro.pdf John Searle: From Speech Acts to Social Reality]
:[http://ontology.buffalo.edu/smith/courses16/Analytic_Metaphysics/2.pdf Slides] [[Contents]]
:[https://www.youtube.com/watch?v=W4Vefe5p6p4 Video]:[http://www.youtube.com/watch?v=AaFnMesr6uQ Massively Planned Social Agency]
:[http://ontology.buffalo.edu/smith/courses16/Analytic_Metaphysics/3.pdf Slides]
:[https://youtu.be/Hk6Df2geYiQ Video]
:See also materials [http://ncorwiki.buffalo.edu/index.php/Workshop_on_BFO_and_the_Ontology_of_Social_Entities_2016 here]

== October 29: The Ontology of Experimentation, Classification and Measurement==

:[http://hl7-watch.blogspot.com/2008/02/weight-of-baby.html The Weight of the Baby]
:[http://hem.passagen.se/ijohansson/function1.pdf Functions, Function Concepts, and Scales]
:[http://ontology.buffalo.edu/smith/courses16/Analytic_Metaphysics/9.ppt Slides]
:[https://www.youtube.com/watch?v=D3Y5sfnvd5Y Video]

== November 5: Organisms and Environments ==
*Biological Environments
*Human Environments
*Environments, Settings and Behavior

== November 12: Terrorism, Wars and Warfighting==

:[http://www.sozphil.uni-leipzig.de/cm/philosophie/files/2013/01/2006b.pdf Defining Terrorism]
:[http://www.casede.org/BibliotecaCasede/SOF_RoleCombatingTOC.pdf#page=157 An Ontological Framework for Understanding the Terror-Crime Nexus]
:[http://militaryontology.com/ Military Ontology]
:[http://ontology.buffalo.edu/smith/courses16/Analytic_Metaphysics/11.pdf Slides]
:[https://www.youtube.com/watch?v=8MlxZtLnshQ Video]

== November 19: ==

== November 26: Presentations of Student Projects 1==

== December 3: Presentations of Student Projects 2==

== Grading and Related Policies and Services ==

All students will be required to take an active part in class discussions throughout the semester and to prepare a paper on some relevant topic. The paper should be submitted in a draft version on or before March 29, and in final form on or before May 3. A powerpoint version will be presented in class in one or other of the two closing sessions .

Your grade will be determined in three equal portions deriving from:
:1. class participation (2.5% per class attended)
:2. paper (3000 words; deadline for draft: March 29; deadline for final version: May 3)
:3. class presentation (graded according to quality of powerpoint slides, quality of delivery, and quality of response to questions)

For policy regarding incompletes see [http://grad.buffalo.edu/Academics/Policies-Procedures/Grading-Procedures.html here]

For academic integrity policy see [http://www.grad.buffalo.edu/policies/academicintegrity.php here]

For accessibility services see [http://www.buffalo.edu/accessibility/servc.php here]