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]  


==August 25, 2014 Classes Begin
== '''The Course''' ==
==September 1, 2014 Labor Day Observed
'''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.
==September 8  LONDON
 
==September 15
The course is built out of on-line video lectures, video presentations created by students, and discussion sessions covering the topics of each lecture.
==September 22  FOIS
 
==September 29
'''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.
==October  6
 
==October 13
'''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.
==October 20
 
==October 27
'''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.
==November  3
==November 10
==November 17
==November 24
==December 1, 2014


<u>[[For Lab sessions]]</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).


----
'''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.


The materials provided below derive from Fall 2013. See [[Ontological Engineering 2013]]
== '''Schedule''' ==


==August 26: Basic Introduction to Ontology ==
==January 28: Basic Introduction to Ontology ==
<!-- *[http://ncor.buffalo.edu/2013/IE500/Videos/IE500-Video1.m4v Video Download]
*[http://stream.buffalo.edu/shared/research/phismith/IE-500/IE500-Video1.m4v Streaming Video]-->


*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?
*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?
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*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]
*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 1: Introduction to Protégé, installation, configuration, and navigation [http://ncor.buffalo.edu/2013/IE500/Labs/Lab-1.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/Labs/Ron-1.mp4 Video]
==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'.


==September 9: An Overview of Ontology Projects in Military Domains==
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.


<!-- *[http://stream.buffalo.edu/shared/research/phismith/IE-500/IE500-Video2.m4v Streaming Video]
[https://buffalo.app.box.com/s/sus1inb6h62u8ifefjjytfummqirqq0c Slides]
*[http://ncor.buffalo.edu/2013/IE500/Videos/IE500-Video2.m4v Video Download]-->


*We will begin with a video [http://www.youtube.com/watch?v=OzW3Gc_yA9A Introduction to Semantic Technology in the DoD Business Mission Area] by Denis Wisnosky]. We will then describe how ontology is being used for the horizontal integration of warfighter intelligence data within the framework of the US Army’s Distributed Common Ground System Standard Cloud (DSC) initiative. We outline how ontologies are being applied to bring about what we call the ‘semantic enhancement’ of data models used within each intelligence discipline. We then show how the strategy can help to overcome tendencies to stovepiping of intelligence data, and thus to help connecting the dots across different information sources.  
[https://www.youtube.com/watch?v=Gh0f2Us0hr0 Video Part 1],
[https://www.youtube.com/watch?v=HDARyJBvnuc Video Part 2]


*4. 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]
==February 9: Introduction to Basic Formal Ontology==
*5. Military Ontology [http://ncor.buffalo.edu/2013/IE500/5-Military-Ontology.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/5-Military-Ontology.mp4 Video]
*6. [http://ncorwiki.buffalo.edu/index.php/Basic_Formal_Ontology_2.0 Basic Formal Ontology] (BFO) [http://ncor.buffalo.edu/2013/IE500/6-BFO.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/6-BFO.mp4 Video]


*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]
:[http://ncor.buffalo.edu/2012/BFO_Tutorial_2012.pptx Slides]
:[http://ncor.buffalo.edu/2017/BFO-Part1.mp4 BFO Part One: Overview of BFO]


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


==September 16: Ontology and Information Engineering in the Healthcare Domains==
:[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]


*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 world of healthcare data management, with special emphasis on the role of ontologies and standard terminologies.
==February 23: Ontology for Systems Engineering (Parts 1 and 2)==


*7. Informatics and Obamacare [http://ncor.buffalo.edu/2013/IE500/7-informatics-obamacare.ppt Slides] [http://www.youtube.com/watch?v=PhW-ix-FoOQ Video]
:[https://buffalo.box.com/s/3ln2y4iwcfhdikvn1xl514qtqx07qopl Slides]
*8. Electronic Diseases [http://ncor.buffalo.edu/2013/IE500/8-e-Iatrogenesis.pptx Slides]
*9. Healthcare Information Management [http://ncor.buffalo.edu/2013/IE500/9-Healthcare-Information-Management.ppt Slides]
*10. Strategies for Data Integration [http://ncor.buffalo.edu/2013/IE500/10-Strategies%20for%20Data%20Integration.pptx Slides]


*Lab 3: Protégé, defining class relationships [http://ncor.buffalo.edu/2013/IE500/Labs/Lab-3.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/Labs/Ron-3.mp4 Video]
:[https://www.youtube.com/watch?v=QGmwIWmyJeg Part 1: Introduction]


*'''[[Lab Note: Steps to Get OWLViz to Function in Protege]]'''
:[https://www.youtube.com/watch?v=9KojcxcIBJs Part 2: Suites of Ontology Modules]


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


==September 23: Use of Ontologies in Tracking Systems ==
:[https://buffalo.box.com/s/3ln2y4iwcfhdikvn1xl514qtqx07qopl Slides]
<!-- *[http://ncor.buffalo.edu/2013/IE500/Videos/IE500-Video4.m4v Video Download]
:[https://www.youtube.com/watch?v=6yYrFcs4MFk Part 3: Functions and Capabilities]
*[http://stream.buffalo.edu/shared/research/phismith/IE-500/IE500-Video1.m4v Streaming Video]-->


*Presenter: [http://www.referent-tracking.com/RTU/?page=ceusters_vita Werner Ceusters]
:[https://youtu.be/2iSCiyJrW8w Part 4: Product Life Cycle]
:[https://www.youtube.com/watch?v=48gi_vOtb34 Part 5: Commodities, Services, Infrastructure]


*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?]]
==March 9: Simple Protege Introduction==


*11. [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]
[https://www.youtube.com/playlist?list=PLea0WJq13cnAfCC0azrCyquCN_tPelJN1 Videos]
*12. [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]
*13. [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 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]
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.
*[http://ncor.buffalo.edu/2013/IE500/Labs/Widget-Ontology.owl Widget Ontology]


----
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.


==September 30: Ontology and the Semantic Web==
==March 16: Capabilities / Emotions / Diagrams ==
<!-- *[http://ncor.buffalo.edu/2013/IE500/Videos/IE500-Video5.m4v Video Download]
*[http://stream.buffalo.edu/shared/research/phismith/IE-500/IE500-Video5.m4v Streaming Video]-->


Presenter: [http://sciencecommons.org/about/whoweare/ruttenberg/ Alan Ruttenberg]
:[https://buffalo.box.com/s/7h75mycfj8aavlf06r197kgsqjf3jk1i Slides]
:[https://buffalo.box.com/s/9eezntwyorb4k0t5ssfbrnhori0621k9 What do IQ tests measure?]


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. We will discuss the goals of the Semantic Web, current technologies, some technological/intellectual sub-communities, and review some applications in biomedicine and other fields.  Topics to be discussed will include: Linked Open Data, The role of ontology, URIs, RDF, OWL, SPARQL, triple stores, and the World Wide WEB Consortium (W3C).
:[https://buffalo.box.com/s/at1oopv9wm1aemgpa6ggxjmh9m6izrpi Slides]
:[https://www.youtube.com/watch?v=18php_34s-M The Emotion Ontology]


*14. Semantic Web Vision and History [http://ncor.buffalo.edu/2013/IE500/14-Semantic-Web-Vision-History.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/14-Semantic-Web.mp4 Video]
:[http://ontology.buffalo.edu/smith/ppt/Diagrams-and-Time.pptx Slides]
*15. Technology of the Semantic Web [http://ncor.buffalo.edu/2013/IE500/15-Technology.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/15-Technology.mp4 Video]
:[https://www.youtube.com/watch?v=AaFnMesr6uQ Diagrams and Time]
*16. Applications [http://ncor.buffalo.edu/2013/IE500/16-Applications.pptx Slides]  


[http://ncor.buffalo.edu/2013/IE500/Ruttenberg-sources Supplementary sources]
==March 23: Spring Recess==
==March 30: Social Acts==


<u>Background Reading</u>
:[http://ontology.buffalo.edu/smith/ppt/Commanding.pptx Slides]
*Tim Berners Lee Scientific American Articles:
:[https://www.youtube.com/watch?v=tHap_q-dUKk Commanding and Other Social Acts]
*:[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)]
*[http://www.w3.org/TR/2008/WD-hcls-kb-20080404/ Advancing translational research with the Semantic Web HCLS Knowledge base]
*[http://goo.gl/j7xS1l Life sciences on the Semantic Web: the Neurocommons and beyond]
*[http://goo.gl/vD1ank MIREOT: the minimum information to reference an external ontology term]
*[https://code.google.com/p/ohd-ontology/ Representing Intracoranal Tooth Restorations in the Ontology for Oral Health and Disease (project home)]
*[http://goo.gl/mwVpu4 BFO2 Draft on Ontobee]
*[https://code.google.com/p/bfo/issues/list BFO2 Project Issue Tracker]
*[http://obofoundry.org/id-policy.shtml OBO Foundry ID Policy]
*[http://www.w3.org/TR/owl2-conformance/ OWL 2 Web Ontology Language Conformance]
*[http://icbo.buffalo.edu/Presentations/Ruttenberg.pdf Introduction to the Ontology for Biomedical Investigations (OBI) and the Information Artifact Ontology (IAO) (tutorial slides)]


*Lab 5: Protégé, annotation properties, and versioning [http://ncor.buffalo.edu/2013/IE500/Labs/Lab-5.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/Labs/Ron-5.mp4 Video]
:[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]


*[http://ncor.buffalo.edu/2013/IE500/Labs/WidgetManufacturingOntology.owl Widget Manufacturing Ontology]
==April 6: Organizations, Philosophy==


----
:[http://ontology.buffalo.edu/16/Organigram.pdf Slides]
:[https://www.youtube.com/watch?v=bp3B2GkgaB8 The Ontology of the Organigram]


==October 7: Military Ontology==
:[Slides]
:[https://www.youtube.com/watch?v=9zJZiFY-ZrE Metaphysics after Darwin]


*17. Barry Smith: Space, Time and BFO [http://ncor.buffalo.edu/2013/IE500/17-Space-time-BFO.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/17-BFO-Space-Time.mp4 Video]
:[https://www.buffalo.edu/capenchair/events/lectures/barry-smith.html Slides]
*18. [[http://militaryontology.org LTC William Mandrick] LTC Mandrick]: Roots of Ontology in the Military [http://ncor.buffalo.edu/2013/IE500/18-Ontology-in-the-Military.pdf Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/18-Military-Roots.mp4 Video]
:[https://www.youtube.com/watch?v=YkYlY2jnRxc The Future of the History of Philosophy]
*19. LTC Mandrick: Operational Ontology: The Future of the Military Decision Making Process (MDMP) [http://ncor.buffalo.edu/2013/IE500/19-Operations.pdf Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/19-Military-Operations.mp4 Video]
*20. Ron Rudnicki: The CUBRC - US Army Ontology Collaboration [http://ncor.buffalo.edu/2013/IE500/20-Ontologies-for-the-Intelligence-Community.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/20-AIRS-ontologies.mp4 Video]


*Lab 6: Quiz - Protégé and OWL
==April 13: Money==


----
:[http://ontology.buffalo.edu/smith/courses16/Analytic_Metaphysics/8.ppt Slides]
:[https://www.youtube.com/watch?v=d-wmjYbcDBg Analytic Metaphysics and Money]


==October 14: An Overview of Ontology Projects in Financial Domains==  
:[https://buffalo.box.com/s/uvbrxdh5j5ehbjh8j7k2c003dskcyb9i Slides]
:[https://www.youtube.com/watch?v=jBWXz-Ot0mI Debate with John Searle on Free-Standing Y-Terms]


*21. Barry Smith: 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]
==April 20: Quantities, Terrorism==
*22. [http://xbrl.squarespace.com/about-the-author/ Charles Hoffman]: An Overview of Ontology Projects in Financial Domains and Digital Financial Reporting [http://ncor.buffalo.edu/2013/IE500/22-FinancialReportOntology.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/22-Overview.mp4 Video]
*23. Charles Hoffman: Financial Report Ontology: The Big Picture [http://ncor.buffalo.edu/2013/IE500/Videos/22a-FRO-Big-Picture.mp4 Video]


Background reading:  
:[http://ontology.buffalo.edu/smith/ppt/Quantities-Lugano-Feb-2017.pptx Slides]
:[https://www.youtube.com/watch?v=xVVUH00cMNY Quantities as Fiat Universals]


"[http://www.amazon.com/XBRL-For-Dummies-Charles-Hoffman/dp/0470499796 XBRL for Dummies]"
:[http://ontology.buffalo.edu/16/Ontology-of-Terrorism.pdf Slides]
:[https://www.youtube.com/watch?v=VtRM4gPl0TU The Ontology of Terrorism]


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


[http://financialreportontology.wikispaces.com/ Background slides on FRO, the Financial Report Ontology]
:[http://ontology.buffalo.edu/smith/ppt/documents/Deontic-Entities-Geneva-July-2016.pdf Slides]
:[https://youtu.be/WIJJlnLLWGU Towards an Ontology of Deontic Entities]


*Lab 7: Introduction to SPARQL [http://ncor.buffalo.edu/2013/IE500/Labs/Lab-7.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/Ron-7.mp4 Video][http://ncor.buffalo.edu/2013/IE500/Labs/Quiz-1-with-Answers.docx Quiz]
:[https://buffalo.box.com/s/mvpsr0lzvkfay10d8v96ifw7pdskumg9 Slides]
:[https://youtu.be/b4kULamlFaM The Ontology of Disease]


----
:[https://buffalo.box.com/s/9rovx4h1yfj4e46ssh498wdkn7uf99or Slides]
:[https://www.youtube.com/watch?v=gc5a0LaXaBo The Glory and Misery of Electronic Health Records ]


==October 21: Ontologies in Manufacturing: Pitfalls and Promise==
==May 4: Student presentations in video format==


*23. [[Leonard F Jacuzzo]]: '''Semantically Enhanced Manufacturing Analytics''' [http://ncor.buffalo.edu/2013/IE500/23-Manufacturing-Analytics.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/23-Manufacturing-Analytics.mp4 Video]
:Hendry Davignon, [https://www.youtube.com/watch?v=42LSenEYLKw&feature=youtu.be Ontology of the US Government]
*24. [[Kumar Madurai]]: '''Linked Data in the Enterprise''' [http://ncor.buffalo.edu/2013/IE500/24-Linked-Data.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/24-Linked-Data.mp4 Video]
:Timothy Schuler, [https://www.youtube.com/watch?v=22J6c0sPgHw Review of Ontologies for Malware Classification]
:Alexander Anderson, [https://youtu.be/jFZQWwESRmw Quantum Waves in BFO]
:Jonathan Vajda, [https://youtu.be/ifLuaBLL8f4 Ontology of the Unconscious]


Ontology shows promise in the manufacturing domain. Foundational ontologies such as BFO allow for robust modeling of an entire product life-cycle, thereby enhancing knowledge management, product development, and process refinement. Automated manufacturing requires data describing each instance of a manufacturing process. Used correctly, this data facilitates predictive analytics and root cause analysis. Process and product ontologies focus analysis helping to avoid spurious correlations. Though Semantic Technology allows for computation utilizing ontologies, the embryonic state of this technology often requires sacrificing ontological rigor to achieve real-time data usage. This two-part lecture explores the promise of ontology in manufacturing and strategies for avoiding pitfalls one can face.
== '''Provisional list of topics''' ==
 
''[[Preliminary Readings on Manufacturing Ontology]]''
 
*Lab 8: Introduction to SPARQL, using select queries to explore DBpedia [http://ncor.buffalo.edu/2013/IE500/Labs/Lab-8.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/Labs/Ron-8.mp4 Video]


: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
----
----


==October 28: Optimization and Fusion==
== '''Student Learning Outcomes''' ==
*25. [http://mceer.buffalo.edu/ee_expertise/member.asp?k=54 Moises Sudit]: Ontology and Human Intelligences in Optimization and Fusion. Parts 1 and 2
         
:[http://ncor.buffalo.edu/2013/IE500/25a-Optimization-and-Fusion.pptx Slides1] [http://ncor.buffalo.edu/2013/IE500/Videos/25a-Optimization-and-Fusion.mp4 Video1]
{| class="wikitable"
:[http://ncor.buffalo.edu/2013/IE500/25b-Optimization-and-Fusion.pptx Slides2] [http://ncor.buffalo.edu/2013/IE500/Videos/25b-Optimization-and-Fusion.mp4 Video2]
|-
*26. Barry Smith: BFO and the Command Post of the Future
! Program Outcomes/Competencies 
:[http://ncor.buffalo.edu/2013/IE500/26-BFO-CPOF.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/26-BFO-CPOF.mp4 Video]
! Instructional Method(s)
*27. Moises Sudit: Ontology and Human Intelligences in Optimization and Fusion. Parts 3 and 4
! Assessment Method(s)
:[http://ncor.buffalo.edu/2013/IE500/27a-Optimization-and-Fusion.pptx Slides3] [http://ncor.buffalo.edu/2013/IE500/Videos/27a-Optimization-and-Fusion.mp4 Video3]
|-
:[http://ncor.buffalo.edu/2013/IE500/27b-Optimization-and-Fusion.pptx Slides4] [http://ncor.buffalo.edu/2013/IE500/Videos/27b-Optimization-and-Fusion.mp4 Video4]
| 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
|}


*Lab 9: SPARQL, extending select queries with filters, grouping, and booleans [http://ncor.buffalo.edu/2013/IE500/Labs/Lab-9.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/Labs/Ron-9.mp4 Video]
=='''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'''==


==November 4: Ontology and Natural Language Processing==
Grading will be based on two factors:  


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


*28. Jillian Chavez: A Survey of Natural Language Processing (NLP) [http://ncor.buffalo.edu/2013/IE500/28-Survey-of-NLP.pptx Slides]
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://ncor.buffalo.edu/2013/IE500/Videos/28a-Introduction.mp4 Introduction]
:[http://ncor.buffalo.edu/2013/IE500/Videos/28b-Tagging.mp4 Tagging]
:[http://ncor.buffalo.edu/2013/IE500/Videos/28c-Parsing-Ontologies.mp4 Parsing and Ontologies]


Jillian Chaves has been a computational linguist/language engineer with CUBRC, Inc., since 2012. She holds a Master’s Degree in Linguistics from the University at Buffalo.
II: preparation of a youtube video and associated documentation (including powerpoint slides and essay).  


*Lab 10: SPARQL, using construct queries to add instance data [http://ncor.buffalo.edu/2013/IE500/Labs/Lab-10.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/Labs/Ron-10.mp4 Video]
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 [http://grad.buffalo.edu/Academics/Policies-Procedures/Grading-Procedures.html Graduate School policies]. Grades will be weighted according to the following breakdown:


==November 11: Ontology and Information Fusion Research ==
Weighting Assignment
:26%    - video summaries (2% per summary)
:14%    - forum participation
:20%    - youtube video
:20%    - powerpoint slides
:20%    - essay / ontology content


*29. [http://hais.pwr.wroc.pl/llinasbio.pdf James Llinas]: Introduction and Overview of Data and Information Fusion [http://ncor.buffalo.edu/2013/IE500/29-Information-Fusion.pptx Slides]
'''Final Grades'''
:Introduction to Information Fusion [http://ncor.buffalo.edu/2013/IE500/Videos/29a-Fusion-Introduction.mp4 Video]
:Multisource Fusion [http://ncor.buffalo.edu/2013/IE500/Videos/29b-Multisource-Fusion.mp4 Video]
:Hard and Soft Fusion [http://ncor.buffalo.edu/2013/IE500/Videos/29c-Hard-and-Soft-Fusion.mp4 Video]


*Lab 11: SPARQL, updating instance data, other Semantic Web tools: Ontofox, D2RQ, and RDFa [http://ncor.buffalo.edu/2013/IE500/Labs/Lab-11.pptx Slides]
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
|}


[http://ncor.buffalo.edu/2013/IE500/Videos/Labs/Ron-11.mp4 Video]
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/2013/IE500/Labs/Individuals.owl Individuals.owl]
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 [http://grad.buffalo.edu/study/progress/policylibrary.a-to-z.html#iugrade here].


==November 18: The Role of Ontologies in Taming Big Data==
=='''Related Policies and Services'''==


*30. 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]
'''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.  
*31. 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]


Tatiana Malyuta, PhD, is Principal Data Architect and Researcher at Data Tactics Corporation and an Associate Professor of the New York College of Technology of CUNY. She is a subject matter expert in data design and data integration. Recently she has been working on integrated data stores on the Cloud within the context of the Army's Distributed Common Ground System (DCGS-A).
'''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].


*Lab 12: D2RQ -- How to Map Models to Ontologies [http://ncor.buffalo.edu/2013/IE500/Labs/Lab-12.pptx Slides] [http://ncor.buffalo.edu/2013/IE500/Videos/Labs/Ron-12.mp4 Video]
== '''Background Reading and Video Materials''' ==


:[[STIDS 2013 | STIDS Background Slides]]
*[http://ontology.buffalo.edu/smith/articles/ontologies.htm Ontology: An Introduction]


----
*[http://ontology.buffalo.edu/smith/articles/Horizontal-integration.pdf Horizontal Integration of Warfighter Intelligence Data]


==November 25: Presentations of Student Projects==
*[http://ncorwiki.buffalo.edu/index.php/Ontology_for_Intelligence,_Defense_and_Security Ontology for Intelligence, Defense and Security (2012)]


*Jordan Feenstra and Yonatan Schreiber: Music Ontology
*[http://ncorwiki.buffalo.edu/index.php/Introduction_to_Prot%C3%A9g%C3%A9 Intoduction to Protégé]
:[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]


*Quiz: SPARQL
*[https://wiki.csc.calpoly.edu/OntologyTutorial/wiki/IntroductionToOntologiesWithProtege Protégé Tutorial]


----
*[http://protegewiki.stanford.edu/wiki/Protege4GettingStarted Getting Started with Protege 4].


==December 2: Presentations of Student Projects==
*[http://owl.cs.manchester.ac.uk/tutorials/protegeowltutorial Matthew Horridge's Protege-OWL Tutorial].


*16:05 Kevin Cui: GIS Data Model Ontology
*[http://militaryontology.org Military 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]
*16:20 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]
*16.35 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]
*16:50 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]
*17:05 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]
*17:20 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]
*17:40 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]
*17:55 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]


[http://ncor.buffalo.edu/2013/IE500/Labs/Quiz-2-with-Answers.docx Quiz 2 with Answers]
*[http://ontology.buffalo.edu/smith/ Streaming video presentations and training courses in ontology]


== '''Background''' ==
*[http://www.sciencedirect.com/science/article/pii/S1877050913000690 Concept Analysis to Enrich Manufacturing Service Capability Models]


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).
*[http://www.sciencedirect.com/science/article/pii/S0166361514000438 Supply Chain Management Ontology]
 
UB ontologists are involved in a variety of national and international projects in the military, healthcare, transport and financial domains. Examples include:
 
*[http://ncor.buffalo.edu/OI2/ Information Integration in Military Intelligence]
 
*[http://www.youtube.com/watch?v=PWUA502hm-k Digitally Connected Medical Devices]
 
*[http://xbrl.squarespace.com/financial-report-ontology/ Digital Financial Reporting]
 
*[http://charleston.afceachapter.org/2012MarchSemantics/009%20-%20Vizenor_STS_20120321.pdf The Next Generation Air Transportation System]


There is an [http://www.academia.edu/2824018/Creating_the_ontologists_of_the_future acknowledged shortage] of persons with ontological engineering expertise in these and related areas.
*[http://link.springer.com/article/10.1007/s40436-014-0073-2 Ontology-based interoperability solutions for textile supply chain]
 
== '''The Course''' ==
This is, as far as we know, the first ever course on Ontological Engineering to be offered in a US university. It will provide an introduction to the methods and uses of ontological engineering, focusing on applications in the areas of military intelligence, healthcare, and finance. It will provide an overview of how ontologies are created and used, together with practical experience in the development of OWL 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. Students may elect to take the course for 2 credit hours without the practical segment.
 
The course will feature occasional guest lectures by leading ontologists from Buffalo and elsewhere, including participants in on-going ontology projects.
 
----
 
== '''Outcomes''' ==
 
 
By the end of the class, students will be able to understand the nature, utility and scope of contemporary ontological engineering. They will understand methods and rules for ontology development; gain experience of what is involved in contributing to ontological initiatives, and learn to understand the benefits and risks of such initiatives.
 
== '''Guidance for Presentations and Reports '''==
 
:Examples of what to include
::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''' ==
 
 
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. 
 
For 3 credit hour students, your grade will be determined in five equal portions deriving from:
: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:
 
:1. class participation (1.5% per class attended),
: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]
 
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]
 
== '''Preliminary Reading and Video Materials''' ==


*[http://ontology.buffalo.edu/smith/articles/ontologies.htm Ontology: An Introduction]
*[http://ontology.buffalo.edu/smith/articles/ontologies.htm Ontology: An Introduction]
Line 397: Line 314:


*[http://www.sciencedirect.com/science/article/pii/S0166361514000438 Supply Chain Management Ontology]
*[http://www.sciencedirect.com/science/article/pii/S0166361514000438 Supply Chain Management Ontology]
*[http://link.springer.com/article/10.1007/s40436-014-0073-2 Ontology-based interoperability solutions for textile supply chain]

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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