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Influenza Ontology

Influenza Ontology. Infectious Disease Ontology Workshop 2008 Burke Squires. Outline. Motivation & Use case Influenza ontology development Challenges Evaluation Joanne Luciano. Motivation. Players BioHealthBase Bioinformatics Resource Center (BRC) (Richard Scheuermann)

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Influenza Ontology

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  1. Influenza Ontology Infectious Disease Ontology Workshop 2008 Burke Squires

  2. Outline • Motivation & Use case • Influenza ontology development • Challenges • Evaluation • Joanne Luciano

  3. Motivation • Players • BioHealthBase Bioinformatics Resource Center (BRC) (Richard Scheuermann) • Centers for Excellence in Influenza Research and Surveillance (CEIRS) • Gemina (Lynn Schriml) • MITRE (Bioforensics) (Joanne Luciano)

  4. Why Influenza Virus? • Infectious disease • 3 Pandemic in 20th Century • 1918 ~40 million deaths worldwide • 1957 • 1968 • H5N1 “Bird Flu” • Antigenic drift (epidemic), shift (pandemic)

  5. Influenza Structure • Single stranded, negative sense RNA virus • Segmented genome • 8 segments • 11 Proteins • Serotype (H5N1) • Hemagluttanin (16 types) • Neuraminidase (9 types)

  6. Influenza Life Cycle

  7. CEIRS Introduction • Areas of Focus • Research • Surveillance • Genotype-phenotype connection • Motivation • Search for “assays of virulence” • Support cross-experiment comparison

  8. CEIRS Use Case • Experimental data (research) • Measures of virulence • Body Weight, IFNg Cytokine Quantification, Lung Titer, TNFa Cytokine Quantification • Need ontology to define, connect assay data

  9. CEIRS Use Case

  10. CEIRS Surveillance Use Case

  11. Outline • Motivation & use case • Influenza ontology development • Challenges • Evaluation

  12. Influenza Ontology Development

  13. Collecting Terms Gemina (26)

  14. Consolidated List of Terms • 200 terms total • Duplicates removed • Culled list of database artifacts • Database permissions • Final total • ~300 terms (with parents, defined classes)

  15. Influenza Ontology Development

  16. Reference Ontologies

  17. Our current status • Basic structure in place • Adding final definitions • Checking each term for reference ontology link • Preparing first draft release Dec. 1

  18. InfluenzO

  19. Assays of Virulence

  20. Outline • Motivation & use case • Influenza ontology development • Challenges • Evaluation

  21. Challenges • Naming the ontology (I-IDO, InfluenzO) • Logistics (geography) • Google Docs works well • Lack of unified tutorial • Difficulty with tools • Mapping of terms to reference ontology • Natural / experimental seperation • How to represent in OBO file?

  22. Evaluation

  23. Core Developers Burke Squires (BHB, CEIRS) Joanne Luciano (MITRE) Lynn Schriml (Gemina) Contributors Richard Scheuermann Meredith Keybl Marc Colosimo Lynette Hirschman Collaborators Eric Bortz (MSSM) Torsten Staab (LANL) Acknowledgements

  24. http://sourceforge.org/projects/InfluenzO

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