Workshop on Infectious Disease Ontology
Detailed Curriculum

The workshop will comprise five sessions:

September 19, 2007:

• 9:00am to 12:30pm - Background Session 1: Introduction to immunology and infectious disease, designed to give an overview of the domain, especially for informatician and ontologist participants.
o Components of the Immune System
o Induction of an Immune Response
o Types of Pathogens and Types of Immune Responses
o Steps in Pathogenesis
o Pathogen Tactics for Evading the Immune Response
o Focus Session on Bacterial Infections

• 2:00pm to 5:30pm - Background Session 2: Introduction to the principles of ontology development.
o What is an ontology?
o Open Biomedical Ontologies (OBO)
o Basic Formal Ontology
o The OBO Foundry Methodology
o Principles of Development

• 7:00pm to 9:00pm - Background Session 3: Ontologies -- the Good, the Bad and the Ugly.
o What are ontologies useful for in biomedicine?
o Success Stories
o Overview of existing resources
o How do we begin to create an ontology of the infectious disease domain within the OBO Foundry framework?

September 20, 2007:

• 9:00am to 12:30pm - Practice Session 1:
o Briefly review BFO/Foundry framework as applied to the Domain of Infectious Disease
o How do we begin to create an ontology of the infectious disease domain within that framework?
o Generate term list
o Map terms to BFO type and identify those terms that are (or should be) contained within current existing Foundry ontologies
o Create a taxonomy for terms not contained in another Foundry ontology

• 2:00pm to 5:30pm - Practice Session 2:
o Identify relations needed
o Define those relations
o Assert those relations in the ontology
o Extend the general infectious disease ontology to a disease-specific ontology by adding disease-specific terms. We will use Tuberculosis as our example.

• 7:00pm to 8:00pm - Practice Session 3:
o This session will focus on critical analysis and on surveying the uses to which the ontology can be put and the next steps in its development.

• 8:00pm – wine and cheese reception