Introduction to Biomedical Ontologies
The National Center for Biomedical Ontology and the University at Buffalo Department of Philosophy sponsored a two-day ontology training event, held in Buffalo, NY on 12-13 April, 2008.
The course was designed to provide a basic introduction to ontology with special reference to applications in the field of biomedical research. It provided an introductory survey of methods and an overview of current developments and best practices in ontology in the life sciences. The course was designed to be of interest to both philosophers and those with a background in medicine or biology.
Handout Materials
1. What is an ontology and what is it useful for?
2. Basic Formal Ontology: An upper-level ontology to support scientific research
Open Biomedical Ontologies (OBO) and the Web Ontology Language (OWL)
The OBO Relation Ontology
An ontological introduction to biomedicine: Defining organism, function and disease
The Gene Ontology (GO), the Foundational Model of Anatomy (FMA) and the Infectious Disease Ontology (IDO)
The OBO Foundry: A suite of biomedical ontologies to support reasoning and data integration
Applications of ontology outside biomedicine
Full deck of slides in handout form:
Reading
General Introduction to Ontology [1]
Video: How to Build an Ontology (with a Case Study on Clinical Trial Ontology) [2]
More Videos and Audios: [3]
Introduction to Basic Formal Ontology [4]
The Gene Ontology and Open Biomedical Ontologies [5]
The Web Ontology Language (OWL) and the Semantic Web [6]
The OBO Foundry: A suite of biomedical ontologies to support reasoning and data integration [7]
Further links
General http://ontology.buffalo.edu/
Basic Formal Ontology http://www.ifomis.org/bfo/
Program
Saturday, April 12
- 8:30am Registration and continental breakfast
- 9:00am Introduction: What is an ontology and what is it useful for?
- 10:30am Coffee
- 10:45am Basic Formal Ontology: An upper-level ontology to support scientific research
- 12:15pm Lunch
- 1:15pm Open Biomedical Ontologies (OBO) and the Web Ontology Language (OWL)
- 2:30pm Coffee
- 3:00pm The OBO Relation Ontology
- 4:30pm Close
Sunday, April 13
- 8:30am Continental breakfast
- 9:00am An ontological introduction to biomedicine: Defining organism, function and disease
- 10:30am Coffee
- 10:45am The Gene Ontology (GO), the Foundational Model of Anatomy (FMA) and the Infectious Disease Ontology (IDO)
- 12:15pm Lunch
- 1:15pm The OBO Foundry: A suite of biomedical ontologies to support reasoning and data integration
- 2:30pm Coffee
- 3:00pm Applications of ontology outside biomedicine
- 4:30pm Close
For University at Buffalo students
This course will serve also as an upper-level undergraduate or introductory graduate course in the University at Buffalo: PHI 499, PHI 599.