Introduction to Biomedical Ontologies

The National Center for Biomedical Ontology and the University at Buffalo Department of Philosophy are sponsoring a two-day training event to be held in Buffalo, NY on 12-13 April, 2008.

• Registration form
• Area hotels
• Poster

This course is designed to provide a basic introduction to ontology with special reference to applications in the field of biomedical research. It will provide an introductory survey of methods and an overview of current developments and best practices in ontology in the life sciences. No prior knowledge of ontology is presupposed. All sessions will be highly interactive and designed to be of interest to both philosophers and those with a background in medicine or biology.

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
• 1:00pm 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 OBO Foundry: A suite of biomedical ontologies to support reasoning and data integration
• 12:15pm Lunch
• 1:00pm The Gene Ontology (GO), the Foundational Model of Anatomy (FMA) and the Infectious Disease Ontology (IDO)
• 2:30pm Coffee
• 3:00pm Applications of ontology outside biomedicine
• 4:30pm Close

Detailed proposals concerning prelimary reading will be sent to all participants in advance of the meeting. For initial orientation, please consult the materials at [1].

A small charge will be made to participants to cover costs. To register interest in participating please send an email to ontology@buffalo.edu. Discounted room rates will be available at local hotels.

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.

Preliminary Reading

General Introduction to Ontology [2]

Video: How to Build an Ontology (with a Case Study on Clinical Trial Ontology) [3]

More Videos and Audios: [4]

Introduction to Basic Formal Ontology [5]

The Gene Ontology and Open Biomedical Ontologies http://www.geneontology.org/GO.doc.shtml

The Web Ontology Language (OWL) and the Semantic Web [6]

The OBO Foundry: A suite of biomedical ontologies to support reasoning and data integration http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf

Further links:

General http://ontology.buffalo.edu/

Basic Formal Ontology http://www.ifomis.org/bfo/