Ontological Engineering

Title: Ontological Engineering

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

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

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

Room: Baldy 200G, UB North Campus

Instructors: Barry Smith and Ron Rudnicki

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

Schedule

For all practical sessions:

• Please install Protégé Desktop 4.3 onto the laptop you will be using for this course:
• First, register here.
• Then continue to the download page and choose from the installers here.
• If you encounter problems, please email Ron Rudnicki.

August 26: 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
• 2. Ontology: From Philosophy to Engineering
• 3. Ontology and the Semantic Web

• Lab 1: Introduction to Protégé, installation, configuration, and navigation

• Slides

September 2: Labor Day (no class)

September 9: An Overview of Ontology Projects in Military Domains

• 4. Basic Formal Ontology (BFO)

BFO is the upper level architecture recommended for use in ontology development projects.

• 5. Overview of Military Ontologies

We will 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

September 16: An Overview of Ontology Projects in 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, will special emphasis on the role of ontologies and standard terminologies.

• Lab 3: Protégé, defining class relationships

September 23: Referent Tracking: Use of Ontologies in Tracking Systems (with Werner Ceusters)

• 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?

• Lab 4: Protégé, additional definitional techniques in OWL

September 30: Ontology and the Semantic Web (with 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 3. 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).

• Lab 5: Protégé, annotation properties, and versioning

October 7: The CUBRC US Army Ontology Collaboration (with LTC William Mandrick)

• LTC Mandrick will describe the roots of ontology in the military. He will discuss the role of ontology and computation in the future of Military Decision Making Process (MDMP).

• Quiz: Protégé and OWL

October 14: An Overview of Ontology Projects in Financial Domains (with Charles Hoffman and Lowell Vizenor)

• Lab 6: Protégé, review and advanced topics

October 21: An Overview of Ontology Projects in Manufacturing and Retail Domains

• Lab 7: Introduction to SPARQL, using select queries to explore DBpedia

October 28: An Overview of Ontology Projects in Task Scheduling Domains and in Alert Systems (with Moises Sudit)

• Lab 8: SPARQL, extending select queries with filters, grouping, and booleans

November 4: Ontology and Natural Language Processing (Ron Rudnicki and Jillian Chaves)

• Lab 9: SPARQL, using construct queries to add instance data

November 11: Ontology and Information Fusion Research (with James Llinas)

• Lab 10: SPARQL, updating instance data

November 18: How to Succeed in Building Ontologies on a Large Scale (Ron Rudnicki and Tanya Malyuta)

• Lab 11: Other Semantic Web tools: Ontofox, D2RQ, and RDFa

November 25: Presentations of Student Projects

• Quiz: SPARQL

December 2: Presentations of Student Projects

Background

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:

• Information Integration in Military Intelligence

• Digitally Connected Medical Devices

• Digital Financial Reporting

• The Next Generation Air Transportation System

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.

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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.

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 November 25),

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 November 25) (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

• Ontology: An Introduction

• Horizontal Integration of Warfighter Intelligence Data

• Ontology for Intelligence, Defense and Security (2012)

• Intoduction to Protégé

• Protégé Tutorial

• Getting Started with Protege 4.

• Matthew Horridge's Protege-OWL Tutorial.

• Military Ontology

• Streaming video presentations and training courses in ontology

• Concept Analysis to Enrich Manufacturing Service Capability Models