Training Workshop

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Event Details


September 19, 2007:

  • 9:00am to 12:30pm - Background Session 1:
  • Introduction to immunology and infectious disease.
  • This session is designed to give an overview of the domain, especially for informatician and ontologist participants. Topics to be covered will include:
  • The Immune System and its Component Parts
  • The Immune Response and How it is Induced
  • Types of Pathogens and Types of Immune Response
  • 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 – what’s good and bad o How do we begin to create an ontology of the infectious disease domain within the OBO Foundry framework? Briefly describe process we will go through the next day. 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? Lay out steps of process and for the day o Example – we can show a small version that includes a small number of terms o Generate term list o Map terms to BFO class and identify those terms that are (or should be) contained within current existing Foundry ontologies o Create taxonomy for terms will not be contained with another Foundry ontology • 2:00pm to 5:30pm - Practice Session 2: o What additional relations are needed o Define those relations o Assert relations o Time permitting, we could extend the general IDO to a disease-specific ontology by adding more specific terms for TB infection. So IDO is like CARO … • 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. • 8:00 until – wine and cheese reception