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Influenza Infectious Disease Ontology (Influenza-IDO)

Influenza Infectious Disease Ontology (Influenza-IDO). Status August 2010. Influenza-IDO Authors. Ryan Brinkman, BCCRC Melanie Courtot, BCCRC Joanne Luciano, Tetherless World Constellation, Rensselaer Polytechnic Institute Lynn Schriml, Univ. of Maryland

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Influenza Infectious Disease Ontology (Influenza-IDO)

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  1. Influenza Infectious Disease Ontology (Influenza-IDO) Status August 2010

  2. Influenza-IDO Authors • Ryan Brinkman, BCCRC • Melanie Courtot, BCCRC • Joanne Luciano, Tetherless World Constellation, Rensselaer Polytechnic Institute • Lynn Schriml, Univ. of Maryland • Richard Scheuermann, Influenza Research Database (IRD) / UT Southwestern • Burke Squires, IRD / UT Southwestern

  3. Domain Requirements • Host and Pathogen: • Anatomy (Host and pathogen) • Taxonomy (Host and pathogen) • Biological Material (Sample) • Infectious Disease (Categorization) • Laboratory Experiment (Scientific procedure) • Surveillance (disease transmission and sample collection)

  4. Influenza-IDO & IDO • Influenza ontology is an extension of IDO • Additionally, Influenza-IDO covers domains outside of IDO (e. g. surveillance)

  5. Example Influenza-IDO Terms • Surveillance (Avian) • Wild • Domestic • Migratory / non-migratory • Virus Experimental Infection Event • Route of delivery *** do you mean transmission vector? *** • Amount delivered (Volume) • Amount delivered (Titer) • Passage time period • Sequence Changes (Analysis) • Virus sequence residue type • Virus sequence residue number • Virus specimen source residue • Post passage residue

  6. Example Influenza-IDO Terms • Surveillance (Avian) • Wild host • A wild host that is a host that is member of a species that remains in their natural state; not tamed or domesticated or cultivated. • Domestic host • A domestic host that is a host that is member of a species that has been tamed by man. • Migratory host • A migratory host is a host that is part of a population that exhibits regular seasonal movement, outward journey followed, some time later, by a return journey. • Non-migratory host • A non-migratory host is a host that is part of a population that does not exhibit regular seasonal movement.

  7. Ontology Enabled Research • Controlled vocabulary enables: • Accurate search & analysis • Precise search & analysis • Compare similar data • Ontological relationships enable: • Quick searches (horizontal) • Quick searches (vertical) (summarization) • Compare dissimilar data

  8. Ontology Enabled Research:Accurate Search & Analysis • Without ontologies: • Searching for host “duck” • Host marked as avian, duck • Duck may or may not be in host field or strain name. • With ontologies: • Search for “duck” will include all duck species • Search for “mallards” with include only relevant data • Compare duck species with ease Duck host: • Duck: 6681 • Mallard: 5236 • Mallard Czech Republic: 1 • Mallard.Maryland: 8 • Dk: 95

  9. Ontology Enabled Research:Precise Search & Analysis • Without ontologies: • Searching for host “duck” • Host searches include non-relevant data and exclude some relevant data • With ontologies: • Search for “duck” will: • include all duck species • NOT include non-duck species • Cleaner data means cleaner statistics False positives: • Ruddy shelduck • Australian shelduck False negatives: • Mallard: 5236 • Mallard Czech Republic: 1 • Mallard.Maryland: 8 • Dk: 95

  10. Ontology Enabled Research:Compare Similar Data • Without ontologies: • Only possible for same investigator / laboratory / assay • With ontologies: • Comparisons enabled for: • Investigators • Laboratories • Assays • Compare historical results to current

  11. Ontology Enabled Research:Quick Searches Across Species • How to analyze duck • Without ontologies: • Search for each species independently: • Shovller • Mallard • Wood duck • Etc. • With ontologies: • Search by order, family, genus and get all species below.

  12. Ontology Enabled Research:Quick Hierarchical Searches • Without ontologies: • Only granularity is avian • With ontologies: • Analysis at any level of taxonomy • Analysis at any level of location

  13. Ontology Enabled Research:Compare Dissimilar Data • Analysis involving chicken data versus all non-chicken avian data • Species Comparison • Search for chicken data • Search for avian data that is NOT chicken • Compare data sets • SFVT example (?) • Compare different assays • Antiviral resistance comparison of lung weight versus mortality

  14. Timeline to Version 1 • Version 1 includes: • CV terms from IRD / CEIRS use cases: • Minimum information for avian surveillance (IRD) • Minimum information for a passage experiment (IRD) • Current Work • Complete remaining definitions for CV terms • Submit new terms to reference ontology • Update / complete OWL ontology file • November 2010 • Submit draft to OBO Foundry • ~100 Terms in Version 1

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