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 Richard Scheuermann, Influenza Research Database (IRD) / UT Southwestern Burke Squires, IRD / UT Southwestern

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)

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

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

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.

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

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

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

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 InvestigatorLaboratoryAssay / Protocol Same InvestigatorLaboratoryAssay / Protocol Same Different Same DifferentSameDifferent Same Different

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. Anatidea (waterfowl) Anas (duck) Anas clypeata (Northern shoveler) Anas platyrhynchos (mallard ducks) Aix Aix sponsa (wood duck)

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 Anatidea (waterfowl) Anas (duck) Anas clypeata (Northern shoveler) Anas platyrhynchos (mallard ducks) Aix Aix sponsa (wood duck)

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

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