Applied Ontology

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Applied Ontology (2016)

Title: PHI 549 Applied Ontology, Spring 2017

Faculty: Barry Smith

Registration: Class# 24197. Registration details for off-campus students are provided under Part Time/Graduate here.

Course Structure: This will be a three credit hour on-line graduate seminar. It will be taught through the medium of a series of 2-hour long videos incorporating presentation of powerpoint slides and question-answer sessions. Links to videos will be distributed according to the schedule below. The final session will consist be structured around youtube videos created by the students in the class.

Course Description: An ontology is a structured collection of terms used to tag data with the goal of making data deriving from heterogeneous sources more easily searchable, comparable or combinable. Ontologies allow information to be shared across communities of scientists with different sorts of expertise. The Gene Ontology, for example, allows researchers on aging to use data from cell biology, yeast biology, cancer biology, genetics, and gerontology, because all of these disciplines create data that are tagged using Gene Ontology terms. The course will provide an introduction to ontology from an application oriented point of view, focusing on the best practices for ontology development and on the development of plug-and-play ontology modules for re-use in different areas. Examples will be drawn primarily from biology and medicine, but no expertise in this disciplines is presupposed.

Schedule The link to the course video for any given week will be provided at 9am on the corresponding Sunday (as listed below). Students are required to watch the video within 48 hours of this posting. Class participants are required to post to the class email forum questions, responses and discussion comments relating to the video from the relevant week.

January 29: Introduction to Ontology

Video Slides
  • A brief history of ontology
  • Semantically enhanced publishing
  • GO: The most successful ontology thus far
  • Aristotle's Metaphysics and Categories
  • The Ontological Square
  • Granular partitions
  • Aristotle vs. Kant
Ontology and Logic Video Slides
  • David Armstrong's Spreadsheet Ontology
  • Fantology: The error of assuming that logic ('F(a)') is the guide to ontological form
  • The confusion of universals and properties
  • Universals and the Boolean organization of the world of classes
  • First order logic with universal terms (FOLWUT)

February 5: The Ontology of Social Reality

Video Slides
  • Speech acts
  • The money in your bank account
  • War and chess
  • Debts
  • Institutions
  • Searle's naturalism and its problems
  • Objects vs. representations
  • Hernando de Soto and The Mystery of Capital
  • Ontology of the credit crunch
Why I Am No Longer a Philosopher (or: Ontology Leaving the Mother Ship of Philosophy) Video Slides
  • How psychology became a scientific discipline independent of philosophy in the 19th century
  • Reasons for founding a new discipline The rise of ontology as an independent discipline
  • Research centers, funding, methods, journals, peer review, national and international conferences, teaching
  • Practical applications of ontology
  • Typical results of the founding of a new discipline
  • Towards a career path for ontologists

February 12: Why Computer Science Needs Philosophy

  • Today's information-driven science faces a vast new problem of data unification
  • In medicine, this problem can be of life-and-death significance
  • The organization that is HL7
  • Ontology 101: Why computer-science ontology needs common sense
  • Does France exist?
  • Why computer scientists prefer a view of ontology as conceptual modeling
  • The alternative: scientific ontologies
  • Towards ontology (science)
Ontology and the Semantic Web Video, Slides
  • Examples of Semantic Web ontologies
  • Simple syllogisms and beyond
  • Problems with XML
  • Clay Shirky: Why the Semantic Web would be a utopia
  • Blooming 'lite' ontologies
  • Why ontology requires thinking
  • To move in the right direction, the Semantic Web needs (inter alia) a guiding upper level ontology

Feb 19: Towards a Standard Upper Level Ontology

Video, Slides
  • Scientific ontologies have special features
  • Building scientific ontologies which work together demands a common set of ontological relations
  • Basic Formal Ontology: benefits of coordination
  • Users of BFO
  • Continuants, occurrents, realizables
  • Specific dependence, generic dependence, information artifacts
  • Dispositions, roles, functions
  • Diseases and disorders: the Ontology of General Medical Science
The Universal Core: Ontology and the US Federal Government Data Integration Initiative Video, Slides, Reading
  • The DoD Net-Centric Data Strategy
  • The Universal Core (UCore) Taxonomy and Semantic Layer
  • Reasoning with OWL DL
  • Managing extension ontologies
  • Example: Command and Control
  • Information entities
  • The UCore change management process
  • How UCore SL helps

Feb 26: 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 [1].
  • In addition to taking Sadawi's course you should also download Protege to your computer from here and experiment with creating simple ontologies of your own and posting them to the web. Include links on the slack page to the ontologies you create.

Mar 5: Ontology and Referent Tracking

  • This video presents a set of rules and best practices for ontology creation, together with examples
  • The three videos below introduce the idea of referent tracking. Where ontologies are descriptions of types (universals and defined classes in reality), a referent tracking system provides a way of referring to and keeping track of the instances of such types. Ontologies and referent tracking systems are thus two sides of a single kind.
  • A referent system (RTS) is designed not merely to keep track of what is the case in reality but also to allow us to capture what is believed to be the case in reality. It also allows us to keep 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.
Basics of Referent Tracking (RT) Video
RT and Video Surveillance Video
RT and Data descriptions Video
  • Reading: How to track absolutely everything?. Note that each time your download this pdf file the copy you create is assigned a new referent tracking ID. This enables Dr Ceusters to keep track of the IP addresses of those who are downloading materials from his site and of which versions of these materials they are downloading at which times.

Mar 12: Basic Formal Ontology Part One

The video material for the period from March 12 through March 26 will cover Basic Formal Ontology as described in the book and in the more technical specification here.

The March 12 content is now available here:

BFO Part One Slides
What BFO is used for
BFO is an upper-level ontology
Ontological realism: an evidence-based strategy for ontology development
Starting point for downward population
Annotation of scientific and administrative data
Part storehouse of lessons learned, part QWERTY keyboard
Basis for common training
Works best under the hood
Brief history of BFO
Aristotle's Ontological Square
Edmund Husserl
The Naive Physics Manifesto
The Gene Ontology and the Foundational Model of Anatomy
BFO's competitors
What BFO, DOLCE, SUMO, CYC have in common
Arguments in favor of using BFO
Important users of BFO
OBO Foundry
NIF Standard
IDO Consortium
Plant Ontology
Universal Core Semantic Layer
How BFO is constructed and maintained
Conservative evolution
Simplicity (two levels; no qualities of qualities)
Strict formality (no overlap with domain ontologies)
Asserted monohierarchy and inferred polyhierarchy
Non-multiplicative (the statue is the portion of clay during the time when the latter has a certain role)
No reductionism, no phenomenalism
No 'context'
No meanings, fictions, non-existents
The Semiotic Triangle
No 'possible worlds'
No abstracta
How to deal with thoughts, beliefs, information artifacts
Overview of BFO 1.0
Instances and universals
Continuants and occurrents
Dependent entities and independent entities
PATO qualities
Different kinds of relations
Symmetry, asymmetry and inverses
The all-some rule
What to do with probabilistic and other some-some relations?
Dispositions and the treatment of modality
Added in BFO 1.1
Generically and specifically dependent continuants, concretizations, and relations of dependence
Information entities

A shorter summary of the March 12-26 material is presented here:

BFO 2.0 Shorter Version Part One
BFO 2.0 Shorter Version Part Two

Mar 19 Spring Recess

Mar 26 Basic Formal Ontology Part Two

  • Apr 2
  • Apr 9
  • Apr 16
  • Apr 23
  • Apr 30
  • May 7 Student video presentations

Example Ontologies

Information Artifact Ontology
Gene Ontology
OBO (Open Biomedical Ontologies) Foundry
The Environment Ontology
Ontology for General Medical Science

Text: Robert Arp, Barry Smith and Andrew Spear, Building Ontologies with Basic Formal Ontology, Cambridge, MA: MIT Press, August 2015

Further readings are provided here:

Requirements: This course is open to all persons with an undergraduate degree and some relevant experience (for example in data scientists, information engineers, terminology researchers). No prior knowledge of ontology is required. In order to receive a grade and course credit students will be required to have reviewed in a timely manner all provided videos and any accompanying recommended reading. Grading will be on the basis of contributions to the on-line class discussion forum and on the quality and content of a 20 minute youtube video (with accompanying essay and powerpoint slide deck) on some topic in the field of applied ontology. Each student will be required to create one such video for presentation in the final class session on May 8. Examples of student videos created in comparable classes in the past are available here and here.

  • Your video should be 20 minutes long; it will be graded on the basis of clarity and force of argument, interestingness of content, and quality of delivery.
  • The video should be based on a powerpoint presentation of approximately 20 slides. The slides should provide a minimal amount of text (using 30 point font or above), together with accompanying graphics, for example charts representing data. You should not read the slides -- rather, you should use the slides as summaries of the successive points you want to make, and present these points ex tempore.
  • The video should be accompanied by an essay presenting the points you make and providing literature references, the whole amounting to at least 3000 words. A short draft of your essay should be submitted to Dr Smith by March 31 at the latest.

Class participants should communicate by email with Dr Smith to determine topic and scope of your video presentation and accompanying materials.

Grading will be based on:

1. forum participation (25%)
2. 20 minute youtube video (25%)
3. associated powerpoint slides (25%)
4. associated essay (25%)

For policy regarding incompletes see here

For academic integrity policy see here