This is a presentation about the construction of the influenza ontology to support Influenza research and surveillance as part of the Genomics for Bio-forensics MITRE sponsored research.
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Case Study 2: UK ■ Outbreak of H5N1 in the UK at a turkey farm Feb 1, 2007 ■ What is the source of the outbreak?
– Contact with infected wild birds? ■ But turkeys were in an enclosed “biosecure” unit ■ No H5N1 detected in the region in the 2 previous months
– Govt. veterinarian suggested turkey meat from Hungary might be source of infection ■ Turkey farm is adjacent to a poultry packing plant that had processed
poultry products from Hungary ■ Hungary had reported an H5N1 outbreak 2 weeks earlier
■ Sequence data showed that strain infecting the turkeys was 99.96% identical to strain that had infected Hungarian birds
■ Conclusion: Infected Hungarian poultry was source of H5N1 infection – Open question (relevant to food defense):
how did H5N1 spread from processing plant to live turkeys?
■ BioHealthBase: NIAID Influenza Database Point of Contact for
– Centers of Excellence for Influenza Research and Surveillance (CEIRS) ■ Research: Emory, Mt Sinai, St. Jude, Univ. of Rochester ■ Surveillance: St. Jude, UCLA, Univ. of Minnesota
– Los Alamos National Laboratory (LANL)
■ Gemina: Category A-C Pathogen Database Point of contact for
– Children’s Hospital Boston – Johns Hopkins University
Initial steps: • Collect metadata terms • Map and align terms • Group related information • Identify and define relationships • Identify external ontologies
Formalize
OBO-Edit: Ontology Editing Tool
Formalize: • Normalize terms into a CV • Issue unique identifiers • Instantiate class hierarchy • Define properties and values • Link to external ontology terms
Status: We have just started the formalization step.