Ontological Engineering 2013

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Course syllabus from Fall 2013

Time: Mondays, 4-6:50pm, Fall 2013

Room: Baldy 200G, UB North Campus

Department of Industrial and Systems Engineering: IE 500 (Section 001). Registration number 24419

Cross-listed with Department of Philosophy: PHI 598. Registration number 24350

Instructors: Barry Smith and Ron Rudnicki

Office hours: By appointment via email at [1] and [2]

For Lab sessions

August 26, 2013: 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?
  • Lab 1: Introduction to Protégé, installation, configuration, and navigation Slides Video

September 9, 2013: An Overview of Ontology Projects in Military Domains

  • We will begin with a video 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.
  • Lab 2: Protégé, building the taxonomy, introduction to defining classes with OWL Slides Video

September 16, 2013: Ontology and Information Engineering in the Healthcare Domains

  • 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.
  • 7. Informatics and Obamacare Slides
  • 8. Electronic Diseases Slides
  • 9. Healthcare Information Management Slides
  • 10. Strategies for Data Integration Slides
  • Lab 3: Protégé, defining class relationships Slides Video

September 23, 2013: Use of Ontologies in Tracking Systems

  • 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?

September 30, 2013: Ontology and the Semantic Web

Presenter: Alan Ruttenberg

The term "Semantic Web" was introduced by Tim Berners-Lee and others in the late 1990's (1, 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).

Supplementary sources

Background Reading

  • Lab 5: Protégé, annotation properties, and versioning Slides Video

October 7, 2013: Military Ontology

  • 17. Barry Smith: Space, Time and BFO Slides Video
  • 18. LTC William Mandrick LTC Mandrick]: Roots of Ontology in the Military Slides Video
  • 19. LTC Mandrick: Operational Ontology: The Future of the Military Decision Making Process (MDMP) Slides Video
  • 20. Ron Rudnicki: The CUBRC - US Army Ontology Collaboration Slides Video
  • Lab 6: Quiz - Protégé and OWL

October 14, 2013: An Overview of Ontology Projects in Financial Domains

  • 21. Barry Smith: An Introduction to BFO's Treatment of Information Artifacts Slides Video
  • 22. Charles Hoffman: An Overview of Ontology Projects in Financial Domains and Digital Financial Reporting Slides Video
  • 23. Charles Hoffman: Financial Report Ontology: The Big Picture Video

Background reading:

"XBRL for Dummies"

Background slides on FIBO, the Financial Industry Business Ontology

Background slides on FRO, the Financial Report Ontology

October 21, 2013: Ontologies in Manufacturing: Pitfalls and Promise

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.

Preliminary Readings on Manufacturing Ontology

  • Lab 8: Introduction to SPARQL, using select queries to explore DBpedia Slides Video

October 28, 2013: Optimization and Fusion

  • 25. Moises Sudit: Ontology and Human Intelligences in Optimization and Fusion. Parts 1 and 2
Slides1 Video1
Slides2 Video2
  • 26. Barry Smith: BFO and the Command Post of the Future
Slides Video
  • 27. Moises Sudit: Ontology and Human Intelligences in Optimization and Fusion. Parts 3 and 4
Slides3 Video3
Slides4 Video4
  • Lab 9: SPARQL, extending select queries with filters, grouping, and booleans Slides Video

November 4, 2013: Ontology and Natural Language Processing

  • 28. Jillian Chavez: A Survey of Natural Language Processing (NLP) Slides
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.

  • Lab 10: SPARQL, using construct queries to add instance data Slides Video

November 11, 2013: Ontology and Information Fusion Research

Introduction to Information Fusion Video
Multisource Fusion Video
Hard and Soft Fusion Video
  • Lab 11: SPARQL, updating instance data, other Semantic Web tools: Ontofox, D2RQ, and RDFa Slides



November 18, 2013: The Role of Ontologies in Taming Big Data

  • 30. Tanya Malyuta (CUNY): Ontologies vs. Data Models Slides Video
  • 31. Tanya Malyuta (CUNY): Horizontal Integration of Intelligence Data Slides 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).

  • Lab 12: D2RQ -- How to Map Models to Ontologies Slides Video
STIDS Background Slides

November 25, 2013: Presentations of Student Projects

  • Jordan Feenstra and Yonatan Schreiber: Music Ontology
  • Yi Yang and Jeon-Young Kang: GIS Ontology
  • David Lominac: Customer Ontology
  • Lucas Mesmer: Manufacturing Ontology
  • Travis Allen: Twitter Ontology
  • Chad Stahl: Chemical Manufacturing Ontology
  • Brian Donohue and Neil Otte: Personality Ontology
  • Quiz: SPARQL

December 2, 2013: Presentations of Student Projects

  • 16:05 Kevin Cui: GIS Data Model Ontology
  • 16:20 Xinnan Peng: Manufacturing Ontology
  • 16.35 John Beverley: Thermodynamic Equilibrium Ontology
  • 16:50 Paul Poenicke: Gettier Problem Ontology
  • 17:05 Adam Houser: Game Artifact Ontology
  • 17:20 William Hughes and Michael Moskal: Unmanned Aerial Vehicle Ontology
  • 17:40 Kanchan Karadkar: Supply Chain Management Ontology
  • 17:55 Norman Sung: Musical Genre Ontology

Quiz 2 with Answers


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).

UB ontologists are involved in a variety of national and international projects in the military, healthcare, transport and financial domains. Examples include:

There is an acknowledged shortage of persons with ontological engineering expertise in these and related areas.

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.


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

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 here

For academic integrity policy see here

For accessibility services see here

Preliminary Reading and Video Materials