Applied Ontology 2018

From NCOR Wiki
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigationJump to search

PHI 598 Registration 24696

Partially co-located with BMI508 Biomedical Ontology Syllabus

An ontology is a structured collection of terms and definitions that is developed with the goal of making data deriving from heterogeneous sources more easily searchable, comparable or combinable. The course will provide an introduction to ontology from an application oriented point of view, including examples in the areas of data science and artificial intelligence. Examples will be drawn from biology and medicine, social science, law, and finance. The course will be of interest not only to philosophers but also to those interested in biomedical informatics and in the computer and information sciences.

Venue: 200G Baldy, UB North Campus

Time: Mondays, 1:00-3:50pm starting August 27, 2018

Faculty: Barry Smith and Werner Ceusters

Background reading:

  • 1. Arp, Spear and Smith, 2016: Building Ontologies with Basic Formal Ontology, MIT Press, 2016
  • 2. Smith, 2003 "Ontology"

August 27: Introduction to Ontology

What is an ontology?
Key elements of an ontology
What are ontologies useful for?

Slides Video

First class assignment: write a 2-page essay summarizing the key elements of an ontology as identified in the lecture and comparing them to the view of an ontology offered in Hoehndorf, Schofield & Gkoutos, 2015). Deadline: noon, September 6.

Advance reading (prior to September 10 lecture): 1. Scheuermann, Ceusters and Smith, 2009. 2. Haendel et. al., 2018

September 3: Labor Day – No class

September 10 Basic Formal Ontology

Top-level ontologies
Introduction to BFO

BFO can be reviewed here

Slides Video

Advance reading (prior to September 24 lecture): SW Smith and Koppel, 2014

September 17: Ontology and Information Engineering in the Healthcare Domain

Ontology look-alikes
Use of ontology and look-alikes in biomedical applications
BFO as benchmark for biomedical Information Engineering (IE)


Second class assignment: Summarize in a 2-page essay the problems discussed in (SW Smith and Koppel, 2014) and describe how Basic Formal Ontology can assist in dealing solving them

Advance reading (prior to October 1 lecture): Merelli, et al, 2014

September 24: Ontology of Disease

Disease from the clinician’s perspective,
Ontological approaches to disease,
The Ontology for General Medical Science


Third class assignment: Summarize in a 2-page essay the issues discussed in pages 16-21 of Haendel et. al., 2018 and describe how the framework offered by Scheuermann, Ceusters and Smith, 2009 might resolve them.

Advance reading (prior to September 17 lecture): Chapters 5 and 6 of Arp, Smith and Spear, 2016

October 1: Disease / Aging / Ontology Building

Ontology of Disease (Continued)

Slides Video

Ontology of Aging

Slides Video

Ontology Building

Slides Video


Toward an Ontological Treatment of Disease and Diagnosis

October 8: Introduction to Protégé

Protégé is the leading open-source ontology editor

This class taught by Brian Donohue

Slides Video

Fourth class assignment: Create a simple ontology using Protégé. Deadline: noon, 25 October.

October 15: Pain / Bruxism / Embryontology

Ontology of Pain

Slides Video


Slides Video


Slides Video


"Ontology of Pain"
"16 Days"

Fifth class assignment: Create a plan for your presentation on December 3

October 22: Joint Doctrine Ontology / Building an Ethical Warfighter / Terrorism

Joint Doctrine Ontology (JDO)

Slides Video

Building an Ethical Warfighter

Slides Video

Ontology of Terrorism

Slides Video


Department of Defense Dictionary of Military and Associated Terms
P. Morossof et al., "Joint Doctrine Ontology: A Benchmark for Military Information Systems Interoperability" (2015)
R. R. Larsen and J. Hastings, "From Affective Science to Psychiatric Disorder: Ontology as a Semantic Bridge" (2018)

October 29: Top-Level Ontologies / The Six-Category Ontology / Truth and Maps

Top-Level Ontologies

Slides Video

The Six-Category Ontology

Slides Video

Truth and the Ontology of Maps

Slides Video


DOLCE: An Upper-Level Ontology
SUMO Suggested Upper Merged Ontology Basic Formal Ontology]

November 5: From Speech Acts to Document Acts / Social Agency / Deontics

From speech acts to document acts

Slides Video

Massively planned social agency

Slides Video

Deontic entities

Slides Video

November 12: Artificial Intelligence, Deep Learning, Machine Learning / Money

Overview of machine learning and other approaches to the exploitation of Big Data (presented by Kevin Keane)
Role of ontology in Data Science
Ontology of money

Slides Video


Barry Smith and John Searle (2003) "The Construction of Social Reality: An Exchange"
Tom Mitchell, "Key Ideas in Machine Learning"
David Donoho, "50 years of Data Science"
G. Marcus (2018), "Deep Learning: A Critical Appraisal"

November 19: The Ontology of the Eruv

The Ontology of the Eruv

Slides Video


The Ontology of Processes and Functions
The Ontology of the Eruv

November 26: Why computer science needs philosophy / Why I am not a Philosopher

Why computer science needs philosophy

Slides Video

Why I am not a philosopher

Slides Video

December 3: Student Projects

1:05pm Botan Dolun: The Metaphysics of States


1:20pm Angie Li: Ontology Representing Human Artificial Reproductive Technologies


1:35pm Zihe Luo: The Music Ontology


1:50pm Jinwei Hu: Patient Conditions: Referent Tracking and Prognostic Terms


2:05pm Alexander Anderson: Quantum Realism


2:20pm Shyamashree Srinha: Opioid Use Disorder in the Light of Ontology


2:40pm William Mangione: The Drug Repurposing Ontology


3:00pm Jonathan Vajda: On the Relation Between a Biospecimen and its Source


3:20pm Eric Merrell: Ontology of Fictional Entities


3:35pm Arlen Brickman: Defining Cancer

Student Learning Outcomes

Program Outcomes/Competencies Instructional Method(s) Assessment Method(s)
The student will acquire a knowledge of current ontology research in biomedical informatics, data fusion, defense and intelligence Video lectures and online discussions Review of submitted content and of participation in class discussions
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

Sep 6 - first class assignment due
Sep 24 - second class assignment due
Oct 15 - third class assignment due
Oct 18 - fourth class assignment due
Oct 25 - Protege class assignment due
Nov 6 - submit a table of contents and 300 word summary plus draft of associated ppt slides
Nov 17 - submit penultimate draft of essay and powerpoint
Dec 4 - submit final version of essay and powerpoint


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:

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 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

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.

Attendance Policy

Students are expected to attend all lectures. For religious observances, university sanctioned events, athletic commitments and family/work obligations/emergencies, absences may be granted upon request but can have an effect on the finally obtained grade (see grading policy) For course cancellation/emergency planning, see the university website for cancellations/delays due to weather or other unforeseen events (

Classroom Decorum

Students are expected to arrive in due time for each class. Some lectures will start with a pre-lecture test to assess the student’s level of preparation for the class. This test contributes to the final grading. Use of cell phones and laptops is allowed for the purposes of the class, but not for private reasons. Phone calls are not allowed.

Background Reading and Video Materials