Advanced Biomedical Ontology

Course Title: Advanced Topics in Biomedical Ontology

Cross-listed: Department of Biomedical Informatics (BMI 708 SEM) and Department of Philosophy (PHI 637 SEM)

Course Subject Code:

Course Number:

Type of Instruction:

Class Number:

Semester:

BMI

708

SEM

to be assigned

Fall of odd years

PHI

TBD

SEM

to be assigned

Fall of odd years

1. Course Information

• Date(s)/Time(s): to be assigned

• Delivery Mode: Traditional

• Number of Credits: 3

• Instructors

Course directors: Biomedical Informatics: Werner Ceusters, MD (contact: 77 Goodell Street, 5th floor, by

appointment only through wceusters@gmail.com)

Philosophy: Barry Smith, PhD (contact: 126 Park Hall, N Campus, by appointment only through

phismith@buffalo.edu)

Lecturers: Werner Ceusters and Barry Smith

2. Course Description

 The course begins with a review of the theories underlying biomedical knowledge representation and ontology. The methods

and tools for applied ontology as well as the management and maintenance of biomedical ontologies will be discussed in

detail including the principles of ontological realism and the implementation thereof in the Basic Formal Ontology (BFO).

Students will gain experience with the Web Ontology Language (OWL) and the limitations thereof, and with utilities to

query ontologies expressed in OWL. The students will learn how to use and evaluate classifiers and their role in

subsumption. They will learn both the transitive and reflexive closure of subsumption and its applied use in ontology

development, maintenance and use. This course also provides an in-depth review of current theories and research underlying

the development of biomedical ontologies as well as a comparative critical analysis of the major current biomedical

ontologies as well as the methods and tools for biomedical ontology development, use and evaluation.

• Course prerequisites: BMI508 or PHI548 or PHI549.