View source for Ontological Engineering

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

[[Ontological Engineering 2018]]

'''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].

'''Instructor''': [http://ontology.buffalo.edu/smith/shortcv.htm Barry Smith]

'''Prerequisites''': Open to all persons with an undergraduate degree.

'''Office hours''': By appointment via email at [mailto:phismith@buffalo.edu 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, [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.

'''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.

== '''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?

*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]

==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.

[https://buffalo.app.box.com/s/sus1inb6h62u8ifefjjytfummqirqq0c Slides]

[https://www.youtube.com/watch?v=Gh0f2Us0hr0 Video Part 1], 
[https://www.youtube.com/watch?v=HDARyJBvnuc Video Part 2]

==February 9: Introduction to 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]

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

:[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]

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

:[https://buffalo.box.com/s/3ln2y4iwcfhdikvn1xl514qtqx07qopl Slides]

:[https://www.youtube.com/watch?v=QGmwIWmyJeg Part 1: Introduction]

:[https://www.youtube.com/watch?v=9KojcxcIBJs Part 2: Suites of Ontology Modules]

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

:[https://buffalo.box.com/s/3ln2y4iwcfhdikvn1xl514qtqx07qopl Slides]
:[https://www.youtube.com/watch?v=6yYrFcs4MFk Part 3: Functions and Capabilities]

:[https://youtu.be/2iSCiyJrW8w Part 4: Product Life Cycle]
:[https://www.youtube.com/watch?v=48gi_vOtb34 Part 5: Commodities, Services, Infrastructure]

==March 9: Simple Protege Introduction==

[https://www.youtube.com/playlist?list=PLea0WJq13cnAfCC0azrCyquCN_tPelJN1 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 [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.

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.

==March 16: Capabilities / Emotions / Diagrams ==

:[https://buffalo.box.com/s/7h75mycfj8aavlf06r197kgsqjf3jk1i 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]

:[http://ontology.buffalo.edu/smith/ppt/Diagrams-and-Time.pptx Slides]
:[https://www.youtube.com/watch?v=AaFnMesr6uQ Diagrams and Time]

==March 23: Spring Recess==
==March 30: Social Acts==

:[http://ontology.buffalo.edu/smith/ppt/Commanding.pptx Slides]
:[https://www.youtube.com/watch?v=tHap_q-dUKk Commanding and Other Social Acts]

:[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]

==April 6: Organizations, Philosophy==

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

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

:[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]

==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]

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

==April 20: Quantities, Terrorism==

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

:[http://ontology.buffalo.edu/16/Ontology-of-Terrorism.pdf Slides]
:[https://www.youtube.com/watch?v=VtRM4gPl0TU The Ontology of Terrorism]

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

:[http://ontology.buffalo.edu/smith/ppt/documents/Deontic-Entities-Geneva-July-2016.pdf Slides]
:[https://youtu.be/WIJJlnLLWGU Towards an Ontology of Deontic Entities]

:[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 ]

==May 4: Student presentations in video format==

:Hendry Davignon, [https://www.youtube.com/watch?v=42LSenEYLKw&feature=youtu.be Ontology of the US Government]
: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]

== '''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''' ==
          
{| 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
|}

=='''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 [http://grad.buffalo.edu/Academics/Policies-Procedures/Grading-Procedures.html 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 [http://grad.buffalo.edu/study/progress/policylibrary.a-to-z.html#iugrade 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 [http://www.buffalo.edu/studentlife/who-we-are/departments/accessibility.html here].

== '''Background Reading and Video Materials''' ==

*[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]

*[http://ncorwiki.buffalo.edu/index.php/Ontology_for_Intelligence,_Defense_and_Security Ontology for Intelligence, Defense and Security (2012)]

*[http://ncorwiki.buffalo.edu/index.php/Introduction_to_Prot%C3%A9g%C3%A9 Intoduction to Protégé]

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

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

*[http://owl.cs.manchester.ac.uk/tutorials/protegeowltutorial Matthew Horridge's Protege-OWL Tutorial].

*[http://militaryontology.org Military Ontology]

*[http://ontology.buffalo.edu/smith/ Streaming video presentations and training courses in ontology]

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

*[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]

*[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]

*[http://ncorwiki.buffalo.edu/index.php/Ontology_for_Intelligence,_Defense_and_Security Ontology for Intelligence, Defense and Security (2012)]

*[http://ncorwiki.buffalo.edu/index.php/Introduction_to_Prot%C3%A9g%C3%A9 Intoduction to Protégé]

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

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

*[http://owl.cs.manchester.ac.uk/tutorials/protegeowltutorial Matthew Horridge's Protege-OWL Tutorial].

*[http://militaryontology.org Military Ontology]

*[http://ontology.buffalo.edu/smith/ Streaming video presentations and training courses in ontology]

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

*[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]