Applied Ontology 2018 - Revision history

Phismith at 20:05, 12 November 2025

2025-11-12T20:05:38Z

← Older revision		Revision as of 20:05, 12 November 2025
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	'''Readings''':		'''Readings''':
	:[~~http~~://www.jcs.mil/Portals/36/Documents/Doctrine/pubs/dictionary.pdf Department of Defense Dictionary of Military and Associated Terms]		[https://www.jcs.mil/Portals/36/Documents/Doctrine/pubs/dictionary.pdf <span style="background-color:#ffff00">Department of Defense Dictionary of Military and Associated Terms</span>]
	:[~~http~~://~~stids.c4i~~.~~gmu~~.~~edu~~/~~papers~~/~~STIDS_2015_T01_Morosoff_etal.pdf~~ P. Morossof et al., "Joint Doctrine Ontology: A Benchmark for Military Information Systems Interoperability" (2015)]		[https://www.researchgate.net/publication/283797643_Joint_Doctrine_Ontology_A_Benchmark_for_Military_Information_Systems_Interoperability <span style="background-color:#ffff00">P. Morossof et al., "Joint Doctrine Ontology: A Benchmark for Military Information Systems Interoperability" (2015)</span>]
	:[https://www.researchgate.net/publication/328145335_From_Affective_Science_to_Psychiatric_Disorder_Ontology_as_a_Semantic_Bridge R. R. Larsen and J. Hastings, "From Affective Science to Psychiatric Disorder: Ontology as a Semantic Bridge" (2018)]		:[https://www.researchgate.net/publication/328145335_From_Affective_Science_to_Psychiatric_Disorder_Ontology_as_a_Semantic_Bridge R. R. Larsen and J. Hastings, "From Affective Science to Psychiatric Disorder: Ontology as a Semantic Bridge" (2018)]

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	Top-Level Ontologies		Top-Level Ontologies

	[https://buffalo.box.com/s/g0wvvijd47yxfcklxfoybkdzc1vaj0tn Slides] [https://www.youtube.com/watch?v=~~P0gV0nCB0ng Video~~]		[https://buffalo.box.com/s/g0wvvijd47yxfcklxfoybkdzc1vaj0tn Slides] [https://www.youtube.com/watch?v= <span style="background-color:#ffff00">Top-Level Ontologies video</span>]

	The Six-Category Ontology		The Six-Category Ontology
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	'''Readings:'''		'''Readings:'''
	:[~~http~~://~~www~~.~~inf~~.~~ed.ac.uk~~/~~teaching~~/~~courses~~/~~kmm/PDF/L7~~-~~DOLCE.pdf~~ DOLCE: An Upper-Level Ontology]		:[https://link.springer.com/chapter/10.1007/978-3-540-34518-0_8 <span style="background-color:#ffff00">DOLCE: An Upper-Level Ontology</span>]
	:[~~http~~://www.adampease.org/OP/ SUMO Suggested Upper Merged Ontology]		:[https://www.adampease.org/OP/ <span style="background-color:#ffff00">SUMO Suggested Upper Merged Ontology</span>]
	:http://ncorwiki.buffalo.edu/index.php/Basic_Formal_Ontology_2.0 Basic Formal Ontology]		:http://ncorwiki.buffalo.edu/index.php/Basic_Formal_Ontology_2.0 Basic Formal Ontology]

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	:Summaries of potential applications of the ontology		:Summaries of potential applications of the ontology

	'''Grading Policy:''' Grading follows standard [http://grad.buffalo.edu/Academics/Policies-Procedures/~~Grading~~-~~Procedures~~.html ~~Graduate School policies~~]. Grades will be weighted according to the following breakdown:		'''Grading Policy:''' Grading follows standard [http://grad.buffalo.edu/Academics/Policies-Procedures/Academic-Integrity.html <span style="background-color:#ffff00">Academic Integrity Policy</span>]. Grades will be weighted according to the following breakdown:

	Weighting Assignment		Weighting Assignment
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	Students are expected to attend all lectures. For religious observances, university sanctioned events, athletic commitments and family/work obligations/emergencies, absences may be granted upon request but can have an effect on the finally obtained grade (see grading policy)		Students are expected to attend all lectures. For religious observances, university sanctioned events, athletic commitments and family/work obligations/emergencies, absences may be granted upon request but can have an effect on the finally obtained grade (see grading policy)
	For course cancellation/emergency planning, see the university website for cancellations/delays due to weather or other unforeseen events (http://emergency.buffalo.edu/campus-weather-alerts.html)		For course cancellation/emergency planning, see the university website for cancellations/delays due to weather or other unforeseen events [http://emergency.buffalo.edu/campus-weather-alerts.html <span style="background-color:#ffff00">Campus Weather Alerts</span>]


	'''Classroom Decorum'''		'''Classroom Decorum'''
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	*[http://ontology.buffalo.edu/smith/articles/ontologies.htm Ontology: An Introduction]		*[http://ontology.buffalo.edu/smith/articles/ontologies.htm Ontology: An Introduction]

	*[https://~~wiki~~.~~csc.calpoly~~.edu/~~OntologyTutorial/wiki/IntroductionToOntologiesWithProtege~~ Protégé Tutorial]		*[https://protege.stanford.edu/ <span style="background-color:#ffff00">Protégé Tutorial</span>]

	*[http://protegewiki.stanford.edu/wiki/Protege4GettingStarted Getting Started with Protege 4].		*[http://protegewiki.stanford.edu/wiki/Protege4GettingStarted Getting Started with Protege 4].
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	*[http://owl.cs.manchester.ac.uk/tutorials/protegeowltutorial Matthew Horridge's Protege-OWL Tutorial].		*[http://owl.cs.manchester.ac.uk/tutorials/protegeowltutorial Matthew Horridge's Protege-OWL Tutorial].

	*[http://~~militaryontology~~.~~org~~ Military Ontology]		*[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-7-part1.pptx <span style="background-color:#ffff00">Military Ontology</span>]

	*[https://www.youtube.com/user/hxo3nql Streaming video presentations and training courses in ontology]		*[https://www.youtube.com/user/hxo3nql Streaming video presentations and training courses in ontology]

Phismith: /* November 26: Why computer science needs philosophy / Why I am not a Philosopher */

2018-12-28T17:27:02Z

November 26: Why computer science needs philosophy / Why I am not a Philosopher

← Older revision		Revision as of 17:27, 28 December 2018
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	Why I am not a philosopher		Why I am not a philosopher

	[https://buffalo.box.com/s/y74umhxrfod6jr5zhh9g659pgea2weld Slides] [https://youtu.be/~~11gDcgiAGPM~~ Video]		[https://buffalo.box.com/s/y74umhxrfod6jr5zhh9g659pgea2weld Slides] [https://youtu.be/e5zjZnbi-ZA Video]

	==December 3: Student Projects ==		==December 3: Student Projects ==

Phismith: /* November 26: Why Computer Science Needs Philosophy / Why I am not a Philosopher */

2018-12-27T22:06:29Z

November 26: Why Computer Science Needs Philosophy / Why I am not a Philosopher

← Older revision		Revision as of 22:06, 27 December 2018
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	:[https://philpapers.org/archive/SMIOPA-3.pdf The Ontology of the Eruv]		:[https://philpapers.org/archive/SMIOPA-3.pdf The Ontology of the Eruv]

	==November 26: Why ~~Computer Science Needs Philosophy~~ / Why I am not a Philosopher ==		==November 26: Why computer science needs philosophy / Why I am not a Philosopher ==

	Why computer science needs philosophy		Why computer science needs philosophy

Phismith: /* November 26: Why Computer Science Needs Philosophy / Why I am not a Philosopher */

2018-12-27T22:05:35Z

November 26: Why Computer Science Needs Philosophy / Why I am not a Philosopher

← Older revision		Revision as of 22:05, 27 December 2018
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	Why I am not a philosopher		Why I am not a philosopher

	[https://buffalo.box.com/s/y74umhxrfod6jr5zhh9g659pgea2weld Slides]		[https://buffalo.box.com/s/y74umhxrfod6jr5zhh9g659pgea2weld Slides] [https://youtu.be/11gDcgiAGPM Video]

	==December 3: Student Projects ==		==December 3: Student Projects ==

Phismith at 13:21, 27 December 2018

2018-12-27T13:21:12Z

← Older revision		Revision as of 13:21, 27 December 2018
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	Advance reading (prior to September 24 lecture): [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3912703/ SW Smith and Koppel, 2014]		Advance reading (prior to September 24 lecture): [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3912703/ SW Smith and Koppel, 2014]

	==September 17: Ontology and Information Engineering ~~(IE)~~ in the Healthcare Domain==		==September 17: Ontology and Information Engineering in the Healthcare Domain==

	:Ontology look-alikes		:Ontology look-alikes
	:Use of ontology and look-alikes in biomedical applications		:Use of ontology and look-alikes in biomedical applications
	:BFO as benchmark for biomedical IE		:BFO as benchmark for biomedical Information Engineering (IE)

	[http://www.referent-tracking.com/RTU/files/BMI508-PHI598-20180917-Ontology-and-Healthcare-IE-covered.pptx Slides]		[http://www.referent-tracking.com/RTU/files/BMI508-PHI598-20180917-Ontology-and-Healthcare-IE-covered.pptx Slides]
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	:[https://philpapers.org/rec/SCHTAO-29 Toward an Ontological Treatment of Disease and Diagnosis]		:[https://philpapers.org/rec/SCHTAO-29 Toward an Ontological Treatment of Disease and Diagnosis]

	==October 8: Protégé ~~Class~~==		==October 8: Introduction to Protégé ==

	[https://protege.stanford.edu/ Protégé] is the leading open-source ontology editor		[https://protege.stanford.edu/ Protégé] is the leading open-source ontology editor
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	Fourth class assignment: Create a simple ontology using Protégé. Deadline: noon, 25 October.		Fourth class assignment: Create a simple ontology using Protégé. Deadline: noon, 25 October.

	==October 15: ~~Ontology of~~ Pain / Bruxism / Embryontology ==		==October 15: Pain / Bruxism / Embryontology ==

	Ontology of Pain		Ontology of Pain
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	Fifth class assignment: Create a plan for your presentation on December 3		Fifth class assignment: Create a plan for your presentation on December 3

	==October 22: Joint Doctrine Ontology / Building an Ethical Warfighter / ~~Ontology of~~ Terrorism==		==October 22: Joint Doctrine Ontology / Building an Ethical Warfighter / Terrorism==

	Joint Doctrine Ontology (JDO)		Joint Doctrine Ontology (JDO)
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	:[https://www.researchgate.net/publication/328145335_From_Affective_Science_to_Psychiatric_Disorder_Ontology_as_a_Semantic_Bridge R. R. Larsen and J. Hastings, "From Affective Science to Psychiatric Disorder: Ontology as a Semantic Bridge" (2018)]		:[https://www.researchgate.net/publication/328145335_From_Affective_Science_to_Psychiatric_Disorder_Ontology_as_a_Semantic_Bridge R. R. Larsen and J. Hastings, "From Affective Science to Psychiatric Disorder: Ontology as a Semantic Bridge" (2018)]

	==October 29: Top-Level Ontologies / The Six-Category Ontology / Truth and ~~the Ontology of~~ Maps==		==October 29: Top-Level Ontologies / The Six-Category Ontology / Truth and Maps==

	Top-Level Ontologies		Top-Level Ontologies
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	:http://ncorwiki.buffalo.edu/index.php/Basic_Formal_Ontology_2.0 Basic Formal Ontology]		:http://ncorwiki.buffalo.edu/index.php/Basic_Formal_Ontology_2.0 Basic Formal Ontology]

	==November 5: From Speech Acts to Document Acts / ~~Massively Planned~~ Social Agency ==		==November 5: From Speech Acts to Document Acts / Social Agency / Deontics ==

	From speech acts to document acts		From speech acts to document acts
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	[https://buffalo.box.com/s/y74umhxrfod6jr5zhh9g659pgea2weld Slides]		[https://buffalo.box.com/s/y74umhxrfod6jr5zhh9g659pgea2weld Slides]

	==December 3: ~~Presentations of student projects~~ ==		==December 3: Student Projects ==

	1:05pm Botan Dolun: The Metaphysics of States		1:05pm Botan Dolun: The Metaphysics of States
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	2:20pm Shyamashree Srinha: Opioid Use Disorder in the		2:20pm Shyamashree Srinha: Opioid Use Disorder in the
	~~light~~ of ~~ontology~~		Light of Ontology

	[https://buffalo.box.com/s/392qu8r1zksf5ezww8zr1aejxa56log9 Slides]		[https://buffalo.box.com/s/392qu8r1zksf5ezww8zr1aejxa56log9 Slides]

Phismith: /* November 12: Artificial Intelligence, Deep Learning, Machine Learning / Money */

2018-12-27T13:18:06Z

November 12: Artificial Intelligence, Deep Learning, Machine Learning / Money

← Older revision		Revision as of 13:18, 27 December 2018
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	:Ontology of money		:Ontology of money
	[https://buffalo.box.com/s/4t7ilrkivp5j3po63fiyklv1uo0cxdwq Slides] [https://www.youtube.com/watch?v=dHo-Tn_v8xM Video]		[https://buffalo.box.com/s/4t7ilrkivp5j3po63fiyklv1uo0cxdwq Slides] [https://www.youtube.com/watch?v=dHo-Tn_v8xM Video]

	'''Readings''':		'''Readings''':
	:[http://ontology.buffalo.edu/smith/articles/searle.pdf Barry Smith and John Searle (2003) "The Construction of Social Reality: An Exchange"]		:[http://ontology.buffalo.edu/smith/articles/searle.pdf Barry Smith and John Searle (2003) "The Construction of Social Reality: An Exchange"]

Phismith: /* November 26: Why Computer Science Needs Philosophy / Why I am not a Philosopher */

2018-12-27T13:17:40Z

November 26: Why Computer Science Needs Philosophy / Why I am not a Philosopher

← Older revision		Revision as of 13:17, 27 December 2018
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	Why computer science needs philosophy		Why computer science needs philosophy

	[https://buffalo.box.com/s/ysavl3d65vyxke9tnt78u9jb7d3mk3pf Slides]		[https://buffalo.box.com/s/ysavl3d65vyxke9tnt78u9jb7d3mk3pf Slides] [https://www.youtube.com/watch?v=0yfhUt1LrIo Video]

	[https://www.youtube.com/watch?v=0yfhUt1LrIo Video]

	Why I am not a philosopher		Why I am not a philosopher

Phismith: /* November 19: Student Contributions / The Ontology of the Eruv */

2018-12-27T13:17:02Z

November 19: Student Contributions / The Ontology of the Eruv

← Older revision		Revision as of 13:17, 27 December 2018
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	:[http://arxiv.org/abs/1801.00631 G. Marcus (2018), "Deep Learning: A Critical Appraisal"]		:[http://arxiv.org/abs/1801.00631 G. Marcus (2018), "Deep Learning: A Critical Appraisal"]

	==November 19: ~~Student Contributions /~~ The Ontology of the Eruv ==		==November 19: The Ontology of the Eruv ==

	~~Student Contributions~~

	The Ontology of the Eruv		The Ontology of the Eruv

Phismith: /* November 26: Why Computer Science Needs Philosophy / Why I am not a Philosopher */

2018-12-27T13:16:28Z

November 26: Why Computer Science Needs Philosophy / Why I am not a Philosopher

← Older revision		Revision as of 13:16, 27 December 2018
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	Why computer science needs philosophy		Why computer science needs philosophy

	[https://buffalo.box.com/s/ysavl3d65vyxke9tnt78u9jb7d3mk3pf Slides]		[https://buffalo.box.com/s/ysavl3d65vyxke9tnt78u9jb7d3mk3pf Slides]

			[https://www.youtube.com/watch?v=0yfhUt1LrIo Video]

	Why I am not a philosopher		Why I am not a philosopher

	[https://buffalo.box.com/s/y74umhxrfod6jr5zhh9g659pgea2weld Slides]		[https://buffalo.box.com/s/y74umhxrfod6jr5zhh9g659pgea2weld Slides]

Phismith: /* December 3: Presentations of student projects */

2018-12-03T20:18:36Z

December 3: Presentations of student projects

← Older revision		Revision as of 20:18, 3 December 2018
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	[https://buffalo.box.com/s/xt1ho7gqfnshm2vg2txxgbs4ogxrx7lc Slides]		[https://buffalo.box.com/s/xt1ho7gqfnshm2vg2txxgbs4ogxrx7lc Slides]

	2:~~55pm~~ Jonathan Vajda: On the Relation Between a Biospecimen and its Source		3:00pm Jonathan Vajda: On the Relation Between a Biospecimen and its Source

	[https://buffalo.box.com/s/5f9854k2zdu1qv8yq7vyg6a933d4ihrq Slides]		[https://buffalo.box.com/s/5f9854k2zdu1qv8yq7vyg6a933d4ihrq Slides]

	3:~~10pm~~ Eric Merrell: Ontology of Fictional Entities		3:20pm Eric Merrell: Ontology of Fictional Entities

	[https://buffalo.box.com/s/g9hl0xcp934pe52mzy1m63b2tp7paei1 Slides]		[https://buffalo.box.com/s/g9hl0xcp934pe52mzy1m63b2tp7paei1 Slides]

	3:~~25pm~~ Arlen Brickman: Defining Cancer		3:35pm Arlen Brickman: Defining Cancer

	== '''Student Learning Outcomes''' ==		== '''Student Learning Outcomes''' ==