Title: PHI 598 / IE 500: Ontological Engineering (Online class), Spring 2018.
- 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 firstname.lastname@example.org
- 1 The Course
- 2 Schedule
- 3 January 28: Basic Introduction to Ontology
- 4 February 2: Introduction to Ontology for Engineers
- 5 February 9: Introduction to Basic Formal Ontology
- 6 February 16: Introduction to Basic Formal Ontology (Part 2)
- 7 February 23: Ontology for Systems Engineering (Parts 1 and 2)
- 8 March 2: Ontology for Systems Engineering (Parts 3. 4 and 5)
- 9 March 9: Simple Protege Introduction
- 10 March 16: Capabilities / Emotions / Diagrams
- 11 March 23: Spring Recess
- 12 March 30: Social Acts
- 13 April 6: Organizations, Philosophy
- 14 April 13: Money
- 15 April 20: Quantities, Terrorism
- 16 April 27: Deontics, Disease, Patient Data
- 17 May 4: Student presentations in video format
- 18 Provisional list of topics
- 19 Student Learning Outcomes
- 20 Important dates
- 21 Grading
- 22 Related Policies and Services
- 23 Background Reading and Video Materials
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 email@example.com. 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.
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 Slides Video
- 2. Ontology: From Philosophy to Engineering Slides Video
- 3. Ontology and the Semantic Web Slides 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.
February 9: Introduction to Basic Formal Ontology
February 16: Introduction to Basic Formal Ontology (Part 2)
February 23: Ontology for Systems Engineering (Parts 1 and 2)
March 2: Ontology for Systems Engineering (Parts 3. 4 and 5)
March 9: Simple Protege Introduction
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
March 23: Spring Recess
March 30: Social Acts
April 6: Organizations, Philosophy
- Metaphysics after Darwin
April 13: Money
April 20: Quantities, Terrorism
April 27: Deontics, Disease, Patient Data
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|
|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 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:
- 26% - video summaries (2% per summary)
- 14% - forum participation
- 20% - youtube video
- 20% - powerpoint slides
- 20% - essay / ontology content
Grade Quality Percentage
|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.