Ontological Engineering: Difference between revisions

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'''Time''': Mondays, 4-6:50pm, Fall 2014
'''Title''': PHI 598 / IE 500: Ontological Engineering (Online class), Spring 2018.


'''Room''': 322 Clemens, UB North Campus
[[Ontological Engineering 2018]]


Department of Industrial and Systems Engineering: IE 500 (Section 001). Registration number [http://www.buffalo.edu/class-schedule?switch=showclass&semester=fall&division=GRAD&dept=IE&regnum=12656 12656]
'''Registration''':
:Class#: [http://www.buffalo.edu/class-schedule?switch=showclass&semester=spring&division=GRAD&dept=PHI&regnum=23854 23854] (PHI)
:Class#: [http://www.buffalo.edu/class-schedule?switch=showclass&semester=spring&division=GRAD&dept=IE&regnum=23450 23450] (ENG)
:Off-campus students: Registration details are provided under Part Time/Graduate [http://studentaccounts.buffalo.edu/tuition/spring.php here].


Cross-listed with:  
'''Instructor''': [http://ontology.buffalo.edu/smith/shortcv.htm Barry Smith]
:Department of Computer Science and Engineering: CSE 510. Registration number [http://www.buffalo.edu/class-schedule?switch=showclass&semester=fall&division=GRAD&dept=CSE&regnum=23684 23684]
:Department of Philosophy: PHI 598. Registration number [http://www.buffalo.edu/class-schedule?switch=showclass&semester=fall&division=GRAD&dept=PHI&regnum=22690 22690]


'''Instructors''': [http://ontology.buffalo.edu/smith Barry Smith] and [http://org.buffalo.edu/rarp/rudnicki_vita.html Ron Rudnicki]
'''Prerequisites''': Open to all persons with an undergraduate degree.


'''Office hours''': By appointment via email at [mailto:phismith@buffalo.edu] and [mailto:rudnicki@cubrc.org]
'''Office hours''': By appointment via email at [mailto:phismith@buffalo.edu phismith@buffalo.edu]  


== '''The Course''' ==
== '''The Course''' ==
This is, as far as we know, the first ever course on Ontological Engineering to be offered in a US university. It was first taught in 2013, and videos, presentations and reading materials from the 2013 class are available here: [[Ontological Engineering 2013]]. The course provides an introduction to the methods and uses of ontological engineering, focusing on applications in areas such as military intelligence, healthcare, and document processing. It will provide an overview of how ontologies are created and used, together with practical experience in the development of ontologies and in the use of associated web technology standards. It will also address some of the human factors underlying the success and failure of ontology projects, including issues of ontology governance and dissemination.
'''Course Description:''' The aim of the course is to provide an introduction to the methods and uses of ontological engineering, focusing on applications in areas such as military intelligence, healthcare, and document processing. It will provide an overview of how ontologies are created and used, together with practical experience in the development of ontologies and in the use of associated web technology standards. It will also address some of the human factors underlying the success and failure of ontology projects, including issues of ontology governance and dissemination.


The course will be built out of 3-hour sessions, each of which will involve 2 hours of lecturing and discussion and 1 hour of practical experience with ontology editing software and other Semantic Web technologies.
The course is built out of on-line video lectures, video presentations created by students, and discussion sessions covering the topics of each lecture.


== '''Background''' ==
'''Course Structure:''' This will be a three credit hour on-line graduate seminar. It will be taught through the medium of a series of videos incorporating presentation of powerpoint slides and accompanying discussion sessions. The final session will be structured around youtube videos created by the students in the class.


Ontologies are an important tool in all areas where data is collected and described by different groups in different ways. Ontologies provide taxonomy-based computerized lexica used to describe diverse bodies of data. They thereby help to aggregate and compare data, to make data more easily discoverable, and to allow large bodies of data to be more effectively searched and analyzed. Ontologies also play an important role in the so-called Semantic Web, where the Web Ontology Language (OWL) forms a central building block in the stack of web technology standards created by the World Wide Web Consortium (W3C).
'''Schedule:''' The link to the course video for any given week will be provided at 9am on the corresponding Friday (as listed below). Students are required to watch this video within 4 days of this posting and to send a ~200 word summary of its content before the end of this period (thus by Tuesday at 9am). This summary should be sent to phismith@buffalo.edu. In addition they should post to the class email forum any questions and comments relating to the video from the relevant week. Questions and comments may be posted at any time during the semester. Your activity on this email forum will be taken into account in determining your grade.


UB ontologists are involved in a variety of national and international projects in the military, healthcare, bioscience, transport and financial domains. There is an [http://www.academia.edu/2824018/Creating_the_ontologists_of_the_future acknowledged shortage] of persons with ontological engineering expertise in all these fields, and in related fields such as journalism, manufacturing and government administration.
'''Text:''' Robert Arp, Barry Smith and Andrew Spear, [https://mitpress.mit.edu/index.php?q=books/building-ontologies-basic-formal-ontology Building Ontologies with Basic Formal Ontology], Cambridge, MA: MIT Press, August 2015.


<u>[http://ncorwiki.buffalo.edu/index.php/Barry_Smith:_Video_Introductions_to_Ontology Smith: Video Introductions to Ontology]</u>
'''Ontologies''' are an important tool in all areas where data is collected and described by different groups in different ways. Ontologies provide taxonomy-based computerized lexica used to describe diverse bodies of data. They thereby help to aggregate and compare data, to make data more easily discoverable, and to allow large bodies of data to be more effectively searched and analyzed. Ontologies also play an important role in the so-called Semantic Web, where the Web Ontology Language (OWL) forms a central building block in the stack of web technology standards created by the World Wide Web Consortium (W3C).


<u>[[For Lab sessions]]</u>
'''Ontology in Buffalo''': UB ontologists are involved in a variety of national and international projects in the military, healthcare, bioscience, engineering, transport and financial domains. There is an [http://www.academia.edu/2824018/Creating_the_ontologists_of_the_future acknowledged shortage] of persons with ontological engineering expertise in all these fields, and in related fields such as journalism, manufacturing and government administration. UB ontologists also work closely with [http://www.cubrc.org/index.php/data-science-and-information-fusion/ontology CUBRC], a Buffalo research, development, testing and systems integration company specializing in the areas of Data Science and Information Fusion; Chemical, Biological and Medical Sciences; and Aeronautics.


<u>[http://ncorwiki.buffalo.edu/index.php?title=Preliminary_Readings_on_Manufacturing_Ontology&action=edit Readings on Manufacturing Ontology]</u>
== '''Schedule''' ==


==August 25: Introduction to Ontology==
==January 28: Basic Introduction to Ontology ==


[http://ncor.buffalo.edu/2014/IE500/1-Introduction.pptx Slides]
*We will begin by addressing questions such as: What is an ontology? What are the differences and interrelations between ontology (philosophy), ontology (science), and ontology (engineering)? How are ontologies used? We will also provide an introduction to Basic Formal Ontology (BFO), focusing on a discussion of the question: What is a plan?


[http://ncor.buffalo.edu/2014/IE500/1-Introduction-Audio.mp4 Audio Recording]
*1. Ontology: A Brief Introduction [http://ncor.buffalo.edu/2013/IE500/1-Introduction-to-Ontology.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/1-Basic-Introduction.mp4 Video]
*2. Ontology: From Philosophy to Engineering [http://ncor.buffalo.edu/2013/IE500/2-From-Philosophy-to-Engineering.ppt Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/2-Ontology-Engineering.mp4 Video]
*3. Ontology and the Semantic Web [http://ncor.buffalo.edu/2013/IE500/3-Ontologies-and-Semantic-Technology.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/3-Semantic-Web.mp4 Video]


'''Lab Slides and Other Materials
==February 2: Introduction to Ontology for Engineers==
* [http://ncor.buffalo.edu/2014/IE500/Labs/Ontology%20Engineering%20Lab%201%20August%2026.pptx Slides]
* [http://ncor.buffalo.edu/2014/IE500/Labs/bfo_classes_only_latest.owl BFO 2.0 Classes Only]
* [http://ncor.buffalo.edu/2014/IE500/Labs/fcauab.pdf Highway Functional Classification]


What is an ontology?
Part 1: Begins with some historical background on the growth of ontology as a discipline on the borderlines of computer science, data science and philosophy. Sketches the development of the Semantic Web and the use of ontologies in the biomedical domain. Concludes with some reflections on the problems associated with the idea of 'linked open data'.


Some simple examples
Part 2: Begins with an outline of Basic Formal Ontology, now used as top-level architecture in more than 200 ontology development projects, across a variety of domains, including engineering. Shows how BFO can be applied to the understanding of the opposition between services and commodities, and also to the understanding of the settings in which services and commodities are sold, delivered, used, maintained, and so forth. Settings in BFO terms are sites, and this allows us to extend our approach to a treatment of the ontology of real estate. The presentation concludes with a discussion of a draft Product Life Cycle Ontology developed within the framework of the NIST Industry Ontology Foundry.


How are ontologies used?
[https://buffalo.app.box.com/s/sus1inb6h62u8ifefjjytfummqirqq0c Slides]


How do ontologies relate to databases?
[https://www.youtube.com/watch?v=Gh0f2Us0hr0 Video Part 1],
[https://www.youtube.com/watch?v=HDARyJBvnuc Video Part 2]


What are the differences and interrelations between ontology (philosophy), ontology (science), and ontology (engineering)?
==February 9: Introduction to Basic Formal Ontology==


The framework we are using: Basic Formal Ontology
:[http://ncor.buffalo.edu/2012/BFO_Tutorial_2012.pptx Slides]
:[http://ncor.buffalo.edu/2017/BFO-Part1.mp4 BFO Part One: Overview of BFO]


'''Background materials from last year's class'''
==February 16: Introduction to Basic Formal Ontology (Part 2)==
*Ontology: A Brief Introduction [http://ncor.buffalo.edu/2013/IE500/1-Introduction-to-Ontology.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/1-Basic-Introduction.mp4 Video]
*Ontology: From Philosophy to Engineering [http://ncor.buffalo.edu/2013/IE500/2-From-Philosophy-to-Engineering.ppt Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/2-Ontology-Engineering.mp4 Video]
*Tanya Malyuta (CUNY): '''Ontologies vs. Data Models''' [http://ncor.buffalo.edu/2013/IE500/30-Horizontal-Integration.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/30-Data-Models-and-Ontologies.mp4 Video]
*Tanya Malyuta (CUNY): '''Horizontal Integration of Intelligence Data''' [http://ncor.buffalo.edu/2013/IE500/31-Ontology_and_Data_Models.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/31-Horizontal-Integration.mp4 Video]
----


==September 8: Big Data and How to Overcome the Problems it Causes==
:[http://ncor.buffalo.edu/2012/BFO_Tutorial_2012.pptx Slides]
:[http://ncor.buffalo.edu/2017/BFO-Part2.mp4 BFO Part Two: Varieties of continuant entities]


[http://ncor.buffalo.edu/2014/IE500/2-Big-Data.pptx Lecture]
==February 23: Ontology for Systems Engineering (Parts 1 and 2)==


[http://ncor.buffalo.edu/2014/IE500/Labs/Ontology%20Engineering%20Lab%202%20September%208.pptx Lab]
:[https://buffalo.box.com/s/3ln2y4iwcfhdikvn1xl514qtqx07qopl Slides]


We are living in a world of big data. To find our way around this world, we need to identify and integrate the data that is important to our needs. The problem is that data is collected always from different perspectives, with different levels of detail, different granularities for example of space and time, and different communities use different technologies and different terminologies when collecting their data. This session provides an introduction to the problems of data fusion. Strategies to address these problems:
:[https://www.youtube.com/watch?v=QGmwIWmyJeg Part 1: Introduction]


*Linked open data
:[https://www.youtube.com/watch?v=9KojcxcIBJs Part 2: Suites of Ontology Modules]
*Mashups
*Crowdsourcing
*[http://en.wikipedia.org/wiki/Data_fusion Data fusion]
*More simple examples
*The Protege Ontology Editor


We outline some of the successes and failures of these different strategies, and introduce some of the features peculiar to the ontological approach underlying much of the work on data fusion taking place in UB, as a preparation for later sessions in this class.
==March 2: Ontology for Systems Engineering (Parts 3. 4 and 5)==


*How to Integrate Data ([http://ncor.buffalo.edu/2013/IE500/4-How-to-integrate-data.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/4-Integrating-Data.mp4 Video] from last year's class)
:[https://buffalo.box.com/s/3ln2y4iwcfhdikvn1xl514qtqx07qopl Slides]
:[https://www.youtube.com/watch?v=6yYrFcs4MFk Part 3: Functions and Capabilities]


*Ron Rudnicki: The CUBRC - US Army Ontology Collaboration ([http://ncor.buffalo.edu/2013/IE500/20-Ontologies-for-the-Intelligence-Community.pptx Slides] and [http://ncor.buffalo.edu/2013/IE500/Videos/20-AIRS-ontologies.mp4 Video] from last year's class)
:[https://youtu.be/2iSCiyJrW8w Part 4: Product Life Cycle]
:[https://www.youtube.com/watch?v=48gi_vOtb34 Part 5: Commodities, Services, Infrastructure]


<!--*Lab 2: Protégé, building the taxonomy, introduction to defining classes with OWL [http://ncor.buffalo.edu/2013/IE500/Labs/Lab-2.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/Labs/Ron-2.mp4 Video]-->
==March 9: Simple Protege Introduction==
 
----


==September 15 An Introduction to Basic Formal Ontology==
[https://www.youtube.com/playlist?list=PLea0WJq13cnAfCC0azrCyquCN_tPelJN1 Videos]


*Why a standard ontology architecture is needed
When watching these videos please bear in mind that we have not introduced in the class so far the specific terminology used by Protege. Most importantly, 'class' in Sadawi's course is what we have been referring to as 'type' or 'universal'. 'Property' is what we have been referring to as 'Relation'. Each property has a domain and a range; for instance the property teaches has the domain teacher and the range student. A guide (probably more than you need) is [https://www.w3.org/TR/owl-guide/ here] and there is also an introduction to the Semantic Web in the Appendix to the BFO book. If there is terminology used in Sadawi's lectures which you think needs explaining please feel free to post a request to the the class email list.
*An introduction to Basic Formal Ontology (BFO)
*BFO and its competitors
*Building ontologies with BFO


*[http://ncor.buffalo.edu/2014/IE500/3-BFO.pptx Slides]
In addition to taking Sadawi's course, the task for this week is to download Protege to your computer from [https://protege.stanford.edu/ here] and experiment with creating a simple ontology of your own and posting it to the class list. This ontology should relate to the topic you have selected for your final class presentation.
*[http://ncor.buffalo.edu/2014/IE500/3-BFO-Video.mp4 Video]
*[http://ncor.buffalo.edu/2014/IE500/5-BFO2_Handout.pdf Handout]
'''Background'''


*[http://www.ifomis.uni-saarland.de/bfo/ BFO website]
==March 16: Capabilities / Emotions / Diagrams ==


'''Lab'''
:[https://buffalo.box.com/s/7h75mycfj8aavlf06r197kgsqjf3jk1i Slides]
*[http://ncor.buffalo.edu/2014/IE500/Labs/Ontology%20Engineering%20Lab%203%20September%2015.pptx Slides]
:[https://buffalo.box.com/s/9eezntwyorb4k0t5ssfbrnhori0621k9 What do IQ tests measure?]


----
:[https://buffalo.box.com/s/at1oopv9wm1aemgpa6ggxjmh9m6izrpi Slides]
:[https://www.youtube.com/watch?v=18php_34s-M The Emotion Ontology]


==September 22: Use of Ontologies in Tracking Systems ==
:[http://ontology.buffalo.edu/smith/ppt/Diagrams-and-Time.pptx Slides]
:[https://www.youtube.com/watch?v=AaFnMesr6uQ Diagrams and Time]


Presenter: [http://www.referent-tracking.com/RTU/?page=ceusters_vita Werner Ceusters]
==March 23: Spring Recess==
==March 30: Social Acts==


A referent tracking system (RTS) is a special kind of digital information system that is designed to keep track of both (1) what is the case in reality and (2) what is expressed in other information systems about what is believed to be the case in reality. An RTS also keeps track of how changes in the information system correspond to changes in the reality outside that system. We will provide an introduction to referent tracking and its implementations. Reading: [[How to track absolutely everything?]]  
:[http://ontology.buffalo.edu/smith/ppt/Commanding.pptx Slides]
:[https://www.youtube.com/watch?v=tHap_q-dUKk Commanding and Other Social Acts]


[http://www.referent-tracking.com/RTU/sendfile/?file=20140922-OntologyClassOnReferentTracking.pptx Slides]
:[http://ontology.buffalo.edu/14/Rijeka/Ontology-of-Documents-May-2014-Rijeka.ppt Slides]
:[https://www.youtube.com/watch?v=4lg4z2up6HI Document Acts and the Ontology of Social Reality]


'''Background'''
==April 6: Organizations, Philosophy==
*[http://ncor.buffalo.edu/2013/IE500/11-Basics-of-Referent-Tracking.pptx Basics of Referent Tracking (RT)] [http://ncor.buffalo.edu/2013/IE500/Videos/11-Referent-Tracking.mp4 Video]
*[http://ncor.buffalo.edu/2013/IE500/12-RT-and-Video-Surveillance.pptx RT and Video Surveillance] [http://ncor.buffalo.edu/2013/IE500/Videos/12-Video-Surveillance.mp4 Video]
*[http://ncor.buffalo.edu/2013/IE500/13-RT-and-Data-descriptions.pptx RT and Data descriptions] [http://ncor.buffalo.edu/2013/IE500/Videos/13-Data-Descriptions.mp4 Video]


'''Lab'''
:[http://ontology.buffalo.edu/16/Organigram.pdf Slides]
*[http://ncor.buffalo.edu/2014/IE500/Labs/Ontology%20Engineering%20Lab%204%20September%2022.pptx Slides]
:[https://www.youtube.com/watch?v=bp3B2GkgaB8 The Ontology of the Organigram]
<!--*Lab 4: Protégé, additional definitional techniques in OWL [http://ncor.buffalo.edu/2013/IE500/Labs/Lab-4.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/Labs/Ron-4.mp4 Video]
*[http://ncor.buffalo.edu/2013/IE500/Labs/Widget-Ontology.owl Widget Ontology]-->


----
:[Slides]
:[https://www.youtube.com/watch?v=9zJZiFY-ZrE Metaphysics after Darwin]


==September 29: How to Build an Ontology==  
:[https://www.buffalo.edu/capenchair/events/lectures/barry-smith.html Slides]
:[https://www.youtube.com/watch?v=YkYlY2jnRxc The Future of the History of Philosophy]


An overview of ontology research in Buffalo
==April 13: Money==


[http://ncor.buffalo.edu/2014/IE500/5-Ontology-in-Buffalo.pptx Slides]
:[http://ontology.buffalo.edu/smith/courses16/Analytic_Metaphysics/8.ppt Slides]
:[https://www.youtube.com/watch?v=d-wmjYbcDBg Analytic Metaphysics and Money]


How to build an ontology 1
:[https://buffalo.box.com/s/uvbrxdh5j5ehbjh8j7k2c003dskcyb9i Slides]
:[https://www.youtube.com/watch?v=jBWXz-Ot0mI Debate with John Searle on Free-Standing Y-Terms]


[http://ncor.buffalo.edu/2014/IE500/5-HowToBuildAnOntology-Sep2014.ppt Slides]
==April 20: Quantities, Terrorism==


[http://ncor.buffalo.edu/2014/IE500/5-HowToBuildAnOntology1-Video.mp4 Video]
:[http://ontology.buffalo.edu/smith/ppt/Quantities-Lugano-Feb-2017.pptx Slides]
:[https://www.youtube.com/watch?v=xVVUH00cMNY Quantities as Fiat Universals]


*Military ontology
:[http://ontology.buffalo.edu/16/Ontology-of-Terrorism.pdf Slides]
::[http://ncor.buffalo.edu/2013/IE500/18-Ontology-in-the-Military.pdf Slides1] [http://ncor.buffalo.edu/2013/IE500/Videos/18-Military-Roots.mp4 Video1] [http://ncor.buffalo.edu/2013/IE500/19-Operations.pdf Slides2] [http://ncor.buffalo.edu/2013/IE500/Videos/19-Military-Operations.mp4 Video2]
:[https://www.youtube.com/watch?v=VtRM4gPl0TU The Ontology of Terrorism]


Lab
==April 27: Deontics, Disease, Patient Data==


*[http://ncor.buffalo.edu/2014/IE500/Labs/Ontology%20Engineering%20Lab%205%20September%2029.pptx Slides]
:[http://ontology.buffalo.edu/smith/ppt/documents/Deontic-Entities-Geneva-July-2016.pdf Slides]
:[https://youtu.be/WIJJlnLLWGU Towards an Ontology of Deontic Entities]


==October 6: Creating Ontologies That Work Together==
:[https://buffalo.box.com/s/mvpsr0lzvkfay10d8v96ifw7pdskumg9 Slides]
:[https://youtu.be/b4kULamlFaM The Ontology of Disease]


How to build an ontology 2
:[https://buffalo.box.com/s/9rovx4h1yfj4e46ssh498wdkn7uf99or Slides]
[http://ncor.buffalo.edu/2014/IE500/7-HowToBuildAnOntology2-Oct2014.ppt Slides]
:[https://www.youtube.com/watch?v=gc5a0LaXaBo The Glory and Misery of Electronic Health Records ]
[http://ncor.buffalo.edu/2014/IE500/6-HowToBuildAnOntology2-Video.mp4 Video]


*The Airs Suite of Ontologies'''
==May 4: Student presentations in video format==
*Annotating Intelligence Data
*Information Artifacts: Publications, databases, passports, emails
*The Email Ontology
*Minimal Information Checklists


<u>Background</u>
:Hendry Davignon, [https://www.youtube.com/watch?v=42LSenEYLKw&feature=youtu.be Ontology of the US Government]
*An Introduction to BFO's Treatment of Information Artifacts [http://ncor.buffalo.edu/2013/IE500/21-IAO-and-BFO.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/21-Information-Artifact-Ontology-BFO-roots.mp4 Video]
:Timothy Schuler, [https://www.youtube.com/watch?v=22J6c0sPgHw Review of Ontologies for Malware Classification]
*[Information Ontologies for the Intelligence Community http://ncorwiki.buffalo.edu/index.php/STIDS_2013]
:Alexander Anderson, [https://youtu.be/jFZQWwESRmw Quantum Waves in BFO]
:Jonathan Vajda, [https://youtu.be/ifLuaBLL8f4 Ontology of the Unconscious]


Lab
== '''Provisional list of topics''' ==


*[http://ncor.buffalo.edu/2014/IE500/Labs/Ontology%20Engineering%20Lab%206%20October%206.pptx Slides]
:Ontology, AI and Robotics
 
:Services, Commodities, Infrastructure
==October 13: Ontology and Information Engineering in the Healthcare Domain==
:Product Life Cycle Ontology  
 
:Ontology and Information Engineering in the Healthcare Domain
Health care today rests increasingly on the proper use of data deriving from different sources (data pertaining to genes, diseases, symptoms, drugs, medical devices, procedures, hospital infections and other adverse events, hospital management, billing, reporting, and many more). We provide an introduction to the ontology of disease, with special reference to the phenomenon of aging.
:The Science of Document Informatics
 
:Finance Ontology
'''Ontology for General Medical Science''' [http://ncor.buffalo.edu/2014/IE500/7-OGMS.ppt Slides] [http://ncor.buffalo.edu/2014/IE500/7-OGMS-Video.mp4 Video]
:The Ontology of Plans
 
:Ontology of Military Logistics
'''Background'''
:Ontology and Intelligence Analysis
*Informatics and Obamacare: [http://ncor.buffalo.edu/2013/IE500/7-informatics-obamacare.ppt Slides] [http://www.youtube.com/watch?v=PhW-ix-FoOQ Video]
:Ontology and Data Fusion
*Electronic Diseases: [http://ncor.buffalo.edu/2013/IE500/8-e-Iatrogenesis.pptx Slides]
:Ontology of Terrorism
*Genomics: [http://www.biomedcentral.com/1471-2105/9/S5/S2 Gene Ontology Annotations]
----
*Electronic Health Records: [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/ Disease and Diagnosis]
*Biodiversity: [http://ncorwiki.buffalo.edu/index.php/Main_Page#Semantics_of_Biodiversity Semantics of Biodiversity]
*Healthcare Information Management: [http://ncor.buffalo.edu/2013/IE500/9-Healthcare-Information-Management.ppt Slides]
*Strategies for Data Integration: [http://ncor.buffalo.edu/2013/IE500/10-Strategies%20for%20Data%20Integration.pptx Slides]
 
Lab
*[http://ncor.buffalo.edu/2014/IE500/Labs/Ontology%20Engineering%20Lab%207%20October%2013.pptx Slides]
 
==October 20: The Science of Document Informatics==
 
What is a document? [http://ncor.buffalo.edu/2014/IE500/8-IAO-and-Ontology-of-Documents.ppt Slides] [http://ncor.buffalo.edu/2014/IE500/8-IAO-and-Ontology-of-Documents.wmv Video (to be edited)]
 
What can we do with documents?
 
What can we do with digital documents that we can't do with paper documents?
 
What is a diagram?
 
How can we extend the technology of optical character recognition (OCR) to comprehend also the graphical content of documents?
 
Background:
*[http://www.jbiomedsem.com/content/5/1/10 Mining images in biomedical publications]
*[http://www.ncbi.nlm.nih.gov/pubmed/23304318 Finding and accessing diagrams in biomedical publications]
*[https://www.youtube.com/watch?v=JWN4Uo-GjjE Document Acts and the Ontology of Social Reality]
 
'''Ontology projects to be discussed'''
 
*[http://ncor.buffalo.edu/2014/IE500/8-Banking-Ontology.pdf Banking Ontology]
*[http://ncor.buffalo.edu/2014/IE500/8-Lathe-Ontology.pptx Lathe ontology]
 
Lab
 
[http://ncor.buffalo.edu/2014/IE500/Labs/Ontology%20Engineering%20Lab%208%20October%2020.pptx Slides]
 
==October 27: The Semantic Web==
 
'''Presentations by Alan Ruttenberg'''
 
*Semantic Web Vision and History [shttp://ncor.buffalo.edu/2014/IE500/9-Vision-History.pptx Slides] [http://ncor.buffalo.edu/2014/IE500/9-Vision-History.wmvVideo]
*Technology of the Semantic Web [http://ncor.buffalo.edu/2014/IE500/9-Semweb-Technical.pptx Slides] [http://ncor.buffalo.edu/2014/IE500/9-Semweb-Technical.wmv Video]
 
'''Background'''
 
*The term "Semantic Web" was introduced by Tim Berners-Lee and others in the late 1990's  ([http://www.w3.org/DesignIssues/Overview.html 1], [http://www.w3.org/DesignIssues/Semantic.html 2]) and first popularized in a paper in 2001 in Scientific American (see below). Berners-Lee summarizes the idea as "a web of data that can be processed directly and indirectly by machines", an extension of the web of documents primarily intended for consumption by people.
 
*Applications [http://ncor.buffalo.edu/2013/IE500/16-Applications.pptx Slides]
 
*Ontology and the Semantic Web [http://ncor.buffalo.edu/2013/IE500/3-Ontologies-and-Semantic-Technology.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/3-Semantic-Web.mp4 Video]
 
*Tim Berners Lee Scientific American Articles :
*:[http://tdo.berkeley.edu/wp-content/uploads/2013/01/SemanticWeb.pdf  The Semantic Web (2001)]
*:[http://www.scientificamerican.com/article.cfm?id=semantic-web-in-actio  The Semantic Web in Action (2007)]
 
==November  3: Ontology Examples==
 
Topics will include:
 
*[http://ncor.buffalo.edu/2014/IE500/10-Questions.pptx Questions (Cameron Bosinski)]
 
::'''Background on Question Ontology'''
::*[http://ontology.buffalo.edu/smith/articles/Questions.pdf Questions: An Essay in Daubertian Phenomenology]
::*[http://www.cs.bham.ac.uk/research/projects/cogaff/misc/question-ontology.pdf Sloman: Ontology for Factual Questions]
::*[http://www.nmmu.ac.za/cyberhunts/bloom.htm Bloom: Taxonomy of Questions]
 
*[http://ncor.buffalo.edu/2014/IE500/10-SEO.pptx School Education (Fumiaki Toyoshima)]
 
*[http://ncor.buffalo.edu/2014/IE500/10-Geographic-Change.pdf Geographic Change (Jeon-Young Kang)]
 
*[http://ncor.buffalo.edu/2014/IE500/10-Victim-Management.pptx Victim Management (Joana Monteiro)]
 
*[http://ncor.buffalo.edu/2014/IE500/10-zhujin_project.owl Community-Based Health Screening (Zhu Jin)]
 
*[http://ncor.buffalo.edu/2014/IE500/10-MASON%20Ontology.pptx Manufacturing Ontology (BS)]
 
::'''Background on Engineering Ontology'''
::*[http://www.researchgate.net/publication/3268400_Multi-Agent_Systems_for_Power_Engineering_ApplicationsPart_II_Technologies_Standards_and_Tools_for_Building_Multi-agent_Systems/file/79e415133819aee475.pdf Ontology of Power Generation]
::*[http://semantic.eurobau.com/ Ontology of Construction]
::*[http://ncorwiki.buffalo.edu/index.php/Preliminary_Readings_on_Manufacturing_Ontology Ontologies of Manufacturing]
 
Lab
 
[http://ncor.buffalo.edu/2014/IE500/Labs/Ontology%20Engineering%20Lab%209%20November%203.pptx Slides]
 
==November 10: Finance Ontology==
 
*[http://ncor.buffalo.edu/2014/IE500/11-Finance.pptx Slides]
'''Background'''
 
*Dennis E. Wisnosky: [https://www.youtube.com/watch?v=OzW3Gc_yA9A Video]
 
*[http://ontolog.cim3.net/file/work/OntologySummit2013/2013-05-02_03_OntologySummit2013_Symposium/Keynote-2_OntologySummit2013_Symposium_FIBO-Briefing--DavidNewman_20130502.pdf Background slides] on FIBO, the Financial Industry Business Ontology
 
==November 17: The Ontology of Plans==
 
'''The Ontology of Planning''' [http://ncor.buffalo.edu/2014/IE500/12-Planning.pptx Slides]


'''Background'''
== '''Student Learning Outcomes''' ==
         
{| class="wikitable"
|-
! Program Outcomes/Competencies 
! Instructional Method(s)
! Assessment Method(s)
|-
| The student will acquire a thorough knowledge of current ontology research in areas relating to engineering, data fusion, defense and intelligence
| Video lectures and online discussions
| Review of submitted online content and of participation in online discussion forum
|-
| The student will acquire experience in ontology development
| Video lectures and critique of successive drafts
| Review of results in the form of xsl spreadsheet or Protégé file
|-
| The student will acquire experience in communicating the results of work on ontology development 
| Creation of youtube presentation and of associated documentation
| Review of results
|}


Erik Thomsen, William Duncan, Tatanya Malyuta and Barry Smith, “[http://ncor.buffalo.edu/mil/STIDS-2014-Living-Plan.pdf A Computational Framework for Living Plan Specification, Execution and Evaluation]”, Proceedings of the Conference on Semantic Technology in Intelligence, Defense and Security (STIDS), George Mason University, Fairfax, VA, November 18-20, 2014.
=='''Important dates'''==
{|
|  Jan 28 || - first video released by Dr Smith at 9am
|-
|  Feb 20 || - about now start to discuss by email the content of your video and essay with Dr Smith
|-
|  Feb 28 || - submit a proposed title and abstract
|-
|  Mar 16 || - create a simple ontology using Protege
|-
|  Mar 31 || - submit a table of contents and 300 word summary plus draft of associated ppt slides
|-
|  Apr 27 || - submit penultimate draft of essay and powerpoint
|-
|  May 4 || - submit final version of essay and powerpoint and upload final version of video to youtube
|}


Kym S. Pohl and Peter Morosoff, "[http://digitalcommons.calpoly.edu/cgi/viewcontent.cgi?article=1099&context=cadrc ICODES: A Load-Planning System that Demonstrates the Value of Ontologies in the Realm of Logistical Command and Control (C2)]", InterSymp-2011, Baden-Baden, Germany, 2 Aug, 2011.
=='''Grading'''==


Jens Pohl, "[http://digitalcommons.calpoly.edu/cgi/viewcontent.cgi?article=1097&context=cadrc An Intelligent Supply Chain Planning and Execution Environment]" Proceedings of InterSymp-2011: Baden-Baden, Germany. Aug. 2011.
Grading will be based on two factors:  


Austin Tate, [http://www.aiai.ed.ac.uk/project/oplan/documents/1996/96-aiia-plan-ontology.pdf Towards a Plan Ontology] (1996)
I: understanding and criticism of the videos presented in classes 1-13


Austin Tate [http://www.aiai.ed.ac.uk/~bat/ontology.html Plan Ontology Page]
All students are required to ingest the content of all videos and to take an active part in on-line discussions throughout the semester.  


[http://www.aiai.ed.ac.uk/~arpi/spar/DOCS/spar-0.1-30oct97.html Planning Initiative Shared Planning and Activity Representation - SPAR] (1997)
II: preparation of a youtube video and associated documentation (including powerpoint slides and essay).


Philip R. Cohen and C. Raymond Perrault, [https://www.cs.rochester.edu/~kautz/Courses/577autumn2007/elements_of_plan_based_theory_speech_acts_cohen.pdf Elements of a Plan‐Based Theory of Speech Acts] (1979). Summarized [http://www.ling.uni-potsdam.de/~garoufi/teaching/planung/06-CohenPerrault.pdf here]
Content and structure of the essay should be discussed with Dr Smith. Where the essay takes the form of the documentation of a specific ontology developed by the student it should include:
:Statement of scope of the ontology
:Summary of existing ontologies in the relevant domain
:Explanation of how your ontology differs from (or incorporates) these ontologies
:Screenshots of parts of the ontology with some examples of important terms and definitions
:Summaries of potential applications of the ontology


[http://www.youtube.com/watch?v=AaFnMesr6uQ Massively Planned Social Agency]
'''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:


==November 24: Presentations of Student Projects 1==
Weighting Assignment
:26%    - video summaries (2% per summary)
:14%    - forum participation
:20%    - youtube video
:20%    - powerpoint slides
:20%    - essay / ontology content


1. Jin Zhu: Community-Based Screening Program for Older Adults
'''Final Grades'''
:[http://ncor.buffalo.edu/2014/IE500/13-1-Zhu.ppt Slides]
:[http://ncor.buffalo.edu/2014/IE500/13-1-Zhu-Ontology.owl Ontology]
:[http://ncor.buffalo.edu/2014/IE500/13-1-Zhu-Report.docx Report]


2. Philip Odonkor: Energy Ontology for Net-Zero Buildings
Grade Quality Percentage
:[http://ncor.buffalo.edu/2014/IE500/13-2-Odonkor.pptx Slides]
{|
:[http://ncor.buffalo.edu/2014/IE500/13-2-NetZOnt.owl Ontology]
|  A || 4.0 || 93.0% -100.00%
:[http://ncor.buffalo.edu/2014/IE500/13-2-Odonkor-Report.pdf Report]
|-
| A- || 3.67 || 90.0% - 92.9%
|-
| B+ || 3.33 || 87.0% - 89.9%
|-
| B || 3.00 || 83.0% - 86.9%
|-
| B- || 2.67 || 80.0% - 82.9%
|-
| C+ || 2.33 || 77.0% - 79.9%
|-
| C || 2.00 || 73.0% - 76.9%
|-
| C- || 1.67 || 70.0% - 72.9%
|-
| D+ || 1.33 || 67.0% - 69.9%
|-
| D || 1.00 || 60.0% - 66.9%
|-
| F || 0 || 59.9% or below
|}


3. Jeon-Young Kang: An Ontology for Capturing Change
An interim grade of Incomplete (I) may be assigned if the student has not completed all requirements for the course. An interim grade of 'I' shall not be assigned to a student who did not attend the course. The default grade accompanying an interim grade of 'I' shall be 'U' and will be displayed on the UB record as 'IU.' The default Unsatisfactory (U) grade shall become the permanent course grade of record if the 'IU' is not changed through formal notice by the instructor upon the student's completion of the course.
:[http://ncor.buffalo.edu/2014/IE500/13-3-Kang.pptx Slides]
4. Joana Monteiro: Victim Management Ontology
:[http://ncor.buffalo.edu/2014/IE500/13-4-Monteiro.pptx Slides]
:[http://ncor.buffalo.edu/2014/IE500/13-4-VictimManagementOntology.owl Ontology]


==December 1: : Presentations of Student Projects 2==
Assignment of an interim 'IU' is at the discretion of the instructor. A grade of 'IU' can be assigned only if successful completion of unfulfilled course requirements can result in a final grade better than the default 'U' grade. The student should have a passing average in the requirements already completed. The instructor shall provide the student specification, in writing, of the requirements to be fulfilled.


1. Lauren Madar: Retail Banking Ontology
The university’s Graduate Incomplete Policy can be found [http://grad.buffalo.edu/study/progress/policylibrary.a-to-z.html#iugrade here].
:[http://ncor.buffalo.edu/2014/IE500/14-1-Retail-Banking.pptx Slides]
:[http://ncor.buffalo.edu/2014/IE500/14-1-Retail-Banking-Ontology Ontology]
:[http://ncor.buffalo.edu/2014/IE500/14-1-RBO-Madar-Report.pdf Report]


2. Cameron Bosinski: Question Ontology
=='''Related Policies and Services'''==
:[http://ncor.buffalo.edu/2014/IE500/14-2-Cameron.pptx Slides]


3. Fumiaki Toyoshima: University Ontology
'''Academic integrity''' is a fundamental university value. Through the honest completion of academic work, students sustain the integrity of the university while facilitating the university's imperative for the transmission of knowledge and culture based upon the generation of new and innovative ideas. See http://grad.buffalo.edu/Academics/Policies-Procedures/Academic-Integrity.html.  
:[http://ncor.buffalo.edu/2014/IE500/14-3-Toyoshima.pptx Slides]
:[http://ncor.buffalo.edu/2014/IE500/14-3-UniversityOntology.owl Ontology]
:[http://ncor.buffalo.edu/2014/IE500/14-3-Toyoshima-Report.docx Report]


4. Keith Fitzsimmons: Lathe Maintenance Ontology
'''Accessibility resources:''' If you have any disability which requires reasonable accommodations to enable you to participate in this course, please contact the Office of Accessibility Resources in 60 Capen Hall, 645-2608 and also the instructor of this course during the first week of class. The office will provide you with information and review appropriate arrangements for reasonable accommodations, which can be found on the web [http://www.buffalo.edu/studentlife/who-we-are/departments/accessibility.html here].
:[http://ncor.buffalo.edu/2014/IE500/14-4-Fitzsimmons.pptx Slides]
:[http://ncor.buffalo.edu/2014/IE500/14-4-LMO.owl Ontology]
:[http://ncor.buffalo.edu/2014/IE500/14-4-Fitzsimmons-LMO-Report.docx Report]


==Examples of Student Projects from 2013==
== '''Background Reading and Video Materials''' ==


*Jordan Feenstra and Yonatan Schreiber: Music Ontology
*[http://ontology.buffalo.edu/smith/articles/ontologies.htm Ontology: An Introduction]
:[http://ncor.buffalo.edu/2013/IE500/Ontologies/MusicTheoryOntology.owl Ontology]
:[http://ncor.buffalo.edu/2013/IE500/Presentations/MusicTheoryOntology.pptx Slides]
:[http://ncor.buffalo.edu/2013/IE500/Reports/Formal-Ontology-of-Music-Theory.docx Report1]
:[http://ncor.buffalo.edu/2013/IE500/Reports/MusTO-Documentation.docx Report2]
*Yi Yang and Jeon-Young Kang: GIS Ontology
:[http://ncor.buffalo.edu/2013/IE500/Ontologies/geo-ontology.owl Ontology]
:[http://ncor.buffalo.edu/2013/IE500/Presentations/Geospatial.pptx Slides]
:[http://ncor.buffalo.edu/2013/IE500/Reports/GIS-Ontology.docx Report]
*David Lominac: Customer Ontology
:[http://ncor.buffalo.edu/2013/IE500/Ontologies/customer-and-invoice-ontology.owl Ontology]
:[http://ncor.buffalo.edu/2013/IE500/Presentations/Customer-&-Invoice-Ontolology.pptx Slides]
:[http://ncor.buffalo.edu/2013/IE500/Reports/Hit-and-Miss.docx Report]
:[http://ncor.buffalo.edu/2013/IE500/Video/Presentations/customer-ontology.mp4 Video]
*Lucas Mesmer: Manufacturing Ontology
:[http://ncor.buffalo.edu/2013/IE500/Ontologies/Mesmer-PMPO.owl Ontology]
:[http://ncor.buffalo.edu/2013/IE500/Presentations/Manufacturing-Mesmer.pptx Slides]
:[http://ncor.buffalo.edu/2013/IE500/Reports/Mesmer-PMPO.docx Report]
:[http://ncor.buffalo.edu/2013/IE500/Video/Presentations/PMPO.mp4 Video]
*Travis Allen: Twitter Ontology
:[http://ncor.buffalo.edu/2013/IE500/Ontologies/Travis-Allen-Twitter-Ontology.owl Ontology]
:[http://ncor.buffalo.edu/2013/IE500/Presentations/Twitter-Ontology.pptx Slides]
:[http://ncor.buffalo.edu/2013/IE500/Reports/Travis-Allen-Twitter-Ontology.docx Report]
:[http://ncor.buffalo.edu/2013/IE500/Video/Presentations/twitter-ontology.mp4 Video]
*Chad Stahl: Chemical Manufacturing Ontology
:[http://ncor.buffalo.edu/2013/IE500/Ontologies/Stahl-Chemical-Manufacturing.owl Ontology]
:[http://ncor.buffalo.edu/2013/IE500/Presentations/Chemical-Manufacturing-Ontology.pptx Slides]
:[http://ncor.buffalo.edu/2013/IE500/Reports/Chemical-Manufacturing-Ontology.docx Report]
*Brian Donohue and Neil Otte: Personality Ontology
:[http://ncor.buffalo.edu/2013/IE500/Ontologies/Personality-Ontology.owl Ontology]
:[http://ncor.buffalo.edu/2013/IE500/Presentations/Personality-Ontology.pptx Slides]
:[http://ncor.buffalo.edu/2013/IE500/Reports/Personality-Assessment-Ontology.docx Report]
*Kevin Cui: GIS Data Model Ontology
:[http://ncor.buffalo.edu/2013/IE500/Ontologies/GIS-Data-Model-Ontology.owl Ontology]
:[http://ncor.buffalo.edu/2013/IE500/Presentations/Cui-Ontology-of-geographic-representation.pptx Slides]
:[http://ncor.buffalo.edu/2013/IE500/Reports/Cui-Geographic-Representation.docx Report]
:[http://ncor.buffalo.edu/2013/IE500/Video/Presentations/cui.mp4 Video]
*Xinnan Peng: Manufacturing Ontology
:[http://ncor.buffalo.edu/2013/IE500/Ontologies/Xinnan-Manufacturing-Ontology.owl Ontology]
:[http://ncor.buffalo.edu/2013/IE500/Presentations/BSMO-Xinnan.pptx Slides]
:[http://ncor.buffalo.edu/2013/IE500/Reports/Peng-Manufacturing-Ontology.pdf Report]
*John Beverley: Thermodynamic Equilibrium Ontology
:[http://ncor.buffalo.edu/2013/IE500/Ontologies/Thermodynamic-Equilibrium-Ontology.owl Ontology]
:[http://ncor.buffalo.edu/2013/IE500/Presentations/Beverley-TEO.pptx Slides]
:[http://ncor.buffalo.edu/2013/IE500/Reports/Thermodynamic-Equilibrium-Ontology.docx Report]
*Paul Poenicke: Gettier Problem Ontology
:[http://ncor.buffalo.edu/2013/IE500/Ontologies/Gettier-Problem-Ontology.owl Ontology]
:[http://ncor.buffalo.edu/2013/IE500/Presentations/Poenicke-Gettier-Problem-Ontology.pptx Slides]
:[http://ncor.buffalo.edu/2013/IE500/Reports/Gettier-Problem-Ontology.docx Report]
*Adam Houser: Game Artifact Ontology
:[http://ncor.buffalo.edu/2013/IE500/Ontologies/DOTA-2-Ontology.owl Ontology]
:[http://ncor.buffalo.edu/2013/IE500/Presentations/Houser-Dota-2.pptx Slides]
:[http://ncor.buffalo.edu/2013/IE500/Reports/Houser-DOTA-2-Ontology.pdf Report]
:[http://ncor.buffalo.edu/2013/IE500/Video/Presentations/dota.mp4 Video]
*William Hughes and Michael Moskal: Unmanned Aerial Vehicle Ontology
:[http://ncor.buffalo.edu/2013/IE500/Ontologies/HughesMoskal_UAVOntology.owl Ontology]
:[http://ncor.buffalo.edu/2013/IE500/Presentations/MoskalHughes_UAVOntology.pptx Slides]
:[http://ncor.buffalo.edu/2013/IE500/Reports/MoskalHughes_UAVOntology.pdf Report]
:[http://ncor.buffalo.edu/2013/IE500/Video/Presentations/moskal-hughes.mp4 Video]
*Kanchan Karadkar: Supply Chain Management Ontology
:[http://ncor.buffalo.edu/2013/IE500/Ontologies/Suppy-Chain-Management-Ontology.owl Ontology]
:[http://ncor.buffalo.edu/2013/IE500/Presentations/Karadkar-Supply-Chain-Management-Ontology.pptx Slides]
:[http://ncor.buffalo.edu/2013/IE500/Reports/Karadkar_SCMO.pdf Report]
:[http://ncor.buffalo.edu/2013/IE500/Video/Presentations/karadkar.mp4 Video]
*Norman Sung: Musical Genre Ontology
:[http://ncor.buffalo.edu/2013/IE500/Ontologies/MusicalGenreOntology.owl Ontology]
:[http://ncor.buffalo.edu/2013/IE500/Presentations/Sung-MusicalGenreOntology.pptx Slides]
:[http://ncor.buffalo.edu/2013/IE500/Reports/Sung-Musical-Genre-Ontology.pdf Report]


== '''Guidance for Presentations and Reports '''==
*[http://ontology.buffalo.edu/smith/articles/Horizontal-integration.pdf Horizontal Integration of Warfighter Intelligence Data]


:Examples of what to include
*[http://ncorwiki.buffalo.edu/index.php/Ontology_for_Intelligence,_Defense_and_Security Ontology for Intelligence, Defense and Security (2012)]
::Statement of scope of the ontology
::The true path rule
::Identification of existing ontologies
::Explanation of how your ontology differs from (or incorporates) these
::Screenshots of parts of the ontology with some examples of important terms and definitions
::Summaries of potential applications of the ontology
:Evaluation
:Completeness


== '''Grading and Related Policies and Services''' ==
*[http://ncorwiki.buffalo.edu/index.php/Introduction_to_Prot%C3%A9g%C3%A9 Intoduction to Protégé]


All students will be required to take an active part in class discussions throughout the semester. In addition they will be required to design and complete an ontology project, including written description, and brief presentation of the project in class. Students enrolled in the practical segment will be required to create a Protégé file to accompany their ontology project, and also to complete quizzes designed to gauge developing competence in the use of the Protégé Ontology Editor and SPARQL query language. 
*[https://wiki.csc.calpoly.edu/OntologyTutorial/wiki/IntroductionToOntologiesWithProtege Protégé Tutorial]


For 3 credit hour students, your grade will be determined in five equal portions deriving from:
*[http://protegewiki.stanford.edu/wiki/Protege4GettingStarted Getting Started with Protege 4].
:1. class participation (1.5% per class attended),
:2. results of two quizzes relating to the lab portion of the course
:3. written description of ontology project (3000 words; deadline December 2),
:4. Protégé ontology file (deadline November 25),
:5. class presentation.  


For 2 credit hour students, your grade is determined as follows:
*[http://owl.cs.manchester.ac.uk/tutorials/protegeowltutorial Matthew Horridge's Protege-OWL Tutorial].


:1. class participation (1.5% per class attended),
*[http://militaryontology.org Military Ontology]
:2. written description of ontology project (4000 words; deadline December 2) (50%),
:3. class presentation (30%).


For policy regarding incompletes see [http://undergrad-catalog.buffalo.edu/policies/grading/explanation.shtml here]
*[http://ontology.buffalo.edu/smith/ Streaming video presentations and training courses in ontology]


For academic integrity policy see [http://www.grad.buffalo.edu/policies/academicintegrity.php here]
*[http://www.sciencedirect.com/science/article/pii/S1877050913000690 Concept Analysis to Enrich Manufacturing Service Capability Models]


For accessibility services see [http://www.buffalo.edu/accessibility/servc.php here]
*[http://www.sciencedirect.com/science/article/pii/S0166361514000438 Supply Chain Management Ontology]


== '''Preliminary Reading and Video Materials''' ==
*[http://link.springer.com/article/10.1007/s40436-014-0073-2 Ontology-based interoperability solutions for textile supply chain]


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

Latest revision as of 23:15, 29 June 2018

Title: PHI 598 / IE 500: Ontological Engineering (Online class), Spring 2018.

Ontological Engineering 2018

Registration:

Class#: 23854 (PHI)
Class#: 23450 (ENG)
Off-campus students: Registration details are provided under Part Time/Graduate here.

Instructor: Barry Smith

Prerequisites: Open to all persons with an undergraduate degree.

Office hours: By appointment via email at phismith@buffalo.edu

The Course

Course Description: The aim of the course is to provide an introduction to the methods and uses of ontological engineering, focusing on applications in areas such as military intelligence, healthcare, and document processing. It will provide an overview of how ontologies are created and used, together with practical experience in the development of ontologies and in the use of associated web technology standards. It will also address some of the human factors underlying the success and failure of ontology projects, including issues of ontology governance and dissemination.

The course is built out of on-line video lectures, video presentations created by students, and discussion sessions covering the topics of each lecture.

Course Structure: This will be a three credit hour on-line graduate seminar. It will be taught through the medium of a series of videos incorporating presentation of powerpoint slides and accompanying discussion sessions. The final session will be structured around youtube videos created by the students in the class.

Schedule: The link to the course video for any given week will be provided at 9am on the corresponding Friday (as listed below). Students are required to watch this video within 4 days of this posting and to send a ~200 word summary of its content before the end of this period (thus by Tuesday at 9am). This summary should be sent to phismith@buffalo.edu. In addition they should post to the class email forum any questions and comments relating to the video from the relevant week. Questions and comments may be posted at any time during the semester. Your activity on this email forum will be taken into account in determining your grade.

Text: Robert Arp, Barry Smith and Andrew Spear, Building Ontologies with Basic Formal Ontology, Cambridge, MA: MIT Press, August 2015.

Ontologies are an important tool in all areas where data is collected and described by different groups in different ways. Ontologies provide taxonomy-based computerized lexica used to describe diverse bodies of data. They thereby help to aggregate and compare data, to make data more easily discoverable, and to allow large bodies of data to be more effectively searched and analyzed. Ontologies also play an important role in the so-called Semantic Web, where the Web Ontology Language (OWL) forms a central building block in the stack of web technology standards created by the World Wide Web Consortium (W3C).

Ontology in Buffalo: UB ontologists are involved in a variety of national and international projects in the military, healthcare, bioscience, engineering, transport and financial domains. There is an acknowledged shortage of persons with ontological engineering expertise in all these fields, and in related fields such as journalism, manufacturing and government administration. UB ontologists also work closely with CUBRC, a Buffalo research, development, testing and systems integration company specializing in the areas of Data Science and Information Fusion; Chemical, Biological and Medical Sciences; and Aeronautics.

Schedule

January 28: Basic Introduction to Ontology

  • We will begin by addressing questions such as: What is an ontology? What are the differences and interrelations between ontology (philosophy), ontology (science), and ontology (engineering)? How are ontologies used? We will also provide an introduction to Basic Formal Ontology (BFO), focusing on a discussion of the question: What is a plan?

February 2: Introduction to Ontology for Engineers

Part 1: Begins with some historical background on the growth of ontology as a discipline on the borderlines of computer science, data science and philosophy. Sketches the development of the Semantic Web and the use of ontologies in the biomedical domain. Concludes with some reflections on the problems associated with the idea of 'linked open data'.

Part 2: Begins with an outline of Basic Formal Ontology, now used as top-level architecture in more than 200 ontology development projects, across a variety of domains, including engineering. Shows how BFO can be applied to the understanding of the opposition between services and commodities, and also to the understanding of the settings in which services and commodities are sold, delivered, used, maintained, and so forth. Settings in BFO terms are sites, and this allows us to extend our approach to a treatment of the ontology of real estate. The presentation concludes with a discussion of a draft Product Life Cycle Ontology developed within the framework of the NIST Industry Ontology Foundry.

Slides

Video Part 1, Video Part 2

February 9: Introduction to Basic Formal Ontology

Slides
BFO Part One: Overview of BFO

February 16: Introduction to Basic Formal Ontology (Part 2)

Slides
BFO Part Two: Varieties of continuant entities

February 23: Ontology for Systems Engineering (Parts 1 and 2)

Slides
Part 1: Introduction
Part 2: Suites of Ontology Modules

March 2: Ontology for Systems Engineering (Parts 3. 4 and 5)

Slides
Part 3: Functions and Capabilities
Part 4: Product Life Cycle
Part 5: Commodities, Services, Infrastructure

March 9: Simple Protege Introduction

Videos

When watching these videos please bear in mind that we have not introduced in the class so far the specific terminology used by Protege. Most importantly, 'class' in Sadawi's course is what we have been referring to as 'type' or 'universal'. 'Property' is what we have been referring to as 'Relation'. Each property has a domain and a range; for instance the property teaches has the domain teacher and the range student. A guide (probably more than you need) is here and there is also an introduction to the Semantic Web in the Appendix to the BFO book. If there is terminology used in Sadawi's lectures which you think needs explaining please feel free to post a request to the the class email list.

In addition to taking Sadawi's course, the task for this week is to download Protege to your computer from here and experiment with creating a simple ontology of your own and posting it to the class list. This ontology should relate to the topic you have selected for your final class presentation.

March 16: Capabilities / Emotions / Diagrams

Slides
What do IQ tests measure?
Slides
The Emotion Ontology
Slides
Diagrams and Time

March 23: Spring Recess

March 30: Social Acts

Slides
Commanding and Other Social Acts
Slides
Document Acts and the Ontology of Social Reality

April 6: Organizations, Philosophy

Slides
The Ontology of the Organigram
[Slides]
Metaphysics after Darwin
Slides
The Future of the History of Philosophy

April 13: Money

Slides
Analytic Metaphysics and Money
Slides
Debate with John Searle on Free-Standing Y-Terms

April 20: Quantities, Terrorism

Slides
Quantities as Fiat Universals
Slides
The Ontology of Terrorism

April 27: Deontics, Disease, Patient Data

Slides
Towards an Ontology of Deontic Entities
Slides
The Ontology of Disease
Slides
The Glory and Misery of Electronic Health Records

May 4: Student presentations in video format

Hendry Davignon, Ontology of the US Government
Timothy Schuler, Review of Ontologies for Malware Classification
Alexander Anderson, Quantum Waves in BFO
Jonathan Vajda, Ontology of the Unconscious

Provisional list of topics

Ontology, AI and Robotics
Services, Commodities, Infrastructure
Product Life Cycle Ontology
Ontology and Information Engineering in the Healthcare Domain
The Science of Document Informatics
Finance Ontology
The Ontology of Plans
Ontology of Military Logistics
Ontology and Intelligence Analysis
Ontology and Data Fusion
Ontology of Terrorism

Student Learning Outcomes

Program Outcomes/Competencies Instructional Method(s) Assessment Method(s)
The student will acquire a thorough knowledge of current ontology research in areas relating to engineering, data fusion, defense and intelligence Video lectures and online discussions Review of submitted online content and of participation in online discussion forum
The student will acquire experience in ontology development Video lectures and critique of successive drafts Review of results in the form of xsl spreadsheet or Protégé file
The student will acquire experience in communicating the results of work on ontology development Creation of youtube presentation and of associated documentation Review of results

Important dates

Jan 28 - first video released by Dr Smith at 9am
Feb 20 - about now start to discuss by email the content of your video and essay with Dr Smith
Feb 28 - submit a proposed title and abstract
Mar 16 - create a simple ontology using Protege
Mar 31 - submit a table of contents and 300 word summary plus draft of associated ppt slides
Apr 27 - submit penultimate draft of essay and powerpoint
May 4 - submit final version of essay and powerpoint and upload final version of video to youtube

Grading

Grading will be based on two factors:

I: understanding and criticism of the videos presented in classes 1-13

All students are required to ingest the content of all videos and to take an active part in on-line discussions throughout the semester.

II: preparation of a youtube video and associated documentation (including powerpoint slides and essay).

Content and structure of the essay should be discussed with Dr Smith. Where the essay takes the form of the documentation of a specific ontology developed by the student it should include:

Statement of scope of the ontology
Summary of existing ontologies in the relevant domain
Explanation of how your ontology differs from (or incorporates) these ontologies
Screenshots of parts of the ontology with some examples of important terms and definitions
Summaries of potential applications of the ontology

Grading Policy: Grading follows standard Graduate School policies. Grades will be weighted according to the following breakdown:

Weighting Assignment

26% - video summaries (2% per summary)
14% - forum participation
20% - youtube video
20% - powerpoint slides
20% - essay / ontology content

Final Grades

Grade Quality Percentage

A 4.0 93.0% -100.00%
A- 3.67 90.0% - 92.9%
B+ 3.33 87.0% - 89.9%
B 3.00 83.0% - 86.9%
B- 2.67 80.0% - 82.9%
C+ 2.33 77.0% - 79.9%
C 2.00 73.0% - 76.9%
C- 1.67 70.0% - 72.9%
D+ 1.33 67.0% - 69.9%
D 1.00 60.0% - 66.9%
F 0 59.9% or below

An interim grade of Incomplete (I) may be assigned if the student has not completed all requirements for the course. An interim grade of 'I' shall not be assigned to a student who did not attend the course. The default grade accompanying an interim grade of 'I' shall be 'U' and will be displayed on the UB record as 'IU.' The default Unsatisfactory (U) grade shall become the permanent course grade of record if the 'IU' is not changed through formal notice by the instructor upon the student's completion of the course.

Assignment of an interim 'IU' is at the discretion of the instructor. A grade of 'IU' can be assigned only if successful completion of unfulfilled course requirements can result in a final grade better than the default 'U' grade. The student should have a passing average in the requirements already completed. The instructor shall provide the student specification, in writing, of the requirements to be fulfilled.

The university’s Graduate Incomplete Policy can be found here.

Related Policies and Services

Academic integrity is a fundamental university value. Through the honest completion of academic work, students sustain the integrity of the university while facilitating the university's imperative for the transmission of knowledge and culture based upon the generation of new and innovative ideas. See http://grad.buffalo.edu/Academics/Policies-Procedures/Academic-Integrity.html.

Accessibility resources: If you have any disability which requires reasonable accommodations to enable you to participate in this course, please contact the Office of Accessibility Resources in 60 Capen Hall, 645-2608 and also the instructor of this course during the first week of class. The office will provide you with information and review appropriate arrangements for reasonable accommodations, which can be found on the web here.

Background Reading and Video Materials

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