Formal Ontology 2017

PHI 548 (seminar, 3 credits). Registration number: 24057

This course is cross-listed with BMI 507, which is offered as part of the newly accredited PhD program in UB's Department of Biomedical Informatics

Time: 4:00-6:50pm, Mondays, Fall Semester 2016

Room: Baldy 200-G, UB North Campus

Instructors: Barry Smith (Philosophy) and Werner Ceusters (Biomedical Informatics)

Office hours: BS: by appointment via email; WC: TBA

Course Description

This course provides an introduction to biomedical ontology. It will review how data and information are generated through biological and biomedical experiments and through patient care, and show how ontologies are used in accessing, maintaining and exploiting the results. We will describe how biomedical ontologies are developed and evaluated and provide a comparative critical analysis of the principal current ontology resources. We will also review the major theories, methods and tools for the development of ontologies, and illustrate how these are being used in different areas of biomedical research and healthcare. On completion of this course students will have a thorough understanding of strategies to manage and exploit biomedical data; they will have a knowledge of categorization, of the philosophy of experimentation, of the philosophy of medicine, and of computer-based reasoning with data.

Recommended background reading

R. Arp, B. Smith, A. D. Spear, Building Ontologies with Basic Formal Ontology

Recommended background video content

Selections from: [1]

8/29/2016 Introduction to Ontology 1: General Overview

Roots of ontology in

• artificial intelligence (Second Naive Physics Manifesto)
• Human Genome Project (Gene Ontology)
• library science (MeSH)
• Semantic Web (OWL)

9/12/2016 Introduction to Ontology 2: Ontology in Buffalo

• Building Ontologies with Basic Formal Ontology
• Open Biomedical Ontologies (OBO) Foundry
• Information Artifact Ontology
• Referent Tracking
• The methodology of ontological realism

9/19/2016 Ontology of Experiments

The generation and dissemination of new knowledge through biomedical research and clinical trials

9/26/2016 Ontology of Clinical Practice

Disease vs. diagnosis; Electronic Health Records and other systems and techniques for modeling, representing and maintaining patient data

10/3/2016 Ontology of Social Entities

Representation of race, gender, and other demographic entities; patient consent; healthcare organizations

10/10/2016 The Gene Ontology and the Open Biomedical Ontologies Foundry

History and current theoretical foundations for the development of effective biomedical ontologies

10/17/2016 Using Ontologies to Represent Biomedical Data, Information and Knowledge

Review of the logical principles for building consistent, structured ontological representations capable of interpretation by both humans and computers

10/24/2016 Representing Types and Representing Instances (WC)

Introduction to Referent Tracking

10/31/2016 Ontology Software

Use of Protege and other tools for ontology editing, search and reasoning

12/5/2016 Student presentations

All students will be required to take an active part in class discussions throughout the semester and to prepare a paper on some relevant topic. The paper should be submitted in a draft version on or before October 31, and in final form on or before December 5. A powerpoint version will be presented in class in one or other of the two closing sessions.

Your grade will be determined in three equal portions deriving from:

1. class participation (2.5% per class attended)

2. paper (3000 words; deadline for draft: March 29; deadline for final version: May 3)

3. class presentation (graded according to quality of powerpoint slides, quality of delivery, and quality of response to questions)

For policy regarding incompletes see here

For academic integrity policy see here

For accessibility services see here