Influenza IDO Status January 2010 Influenza Ontology Developers Melanie Courtot, BCCRC Joanne Luciano, Predictive Medicine, Inc. Lynn Schriml, Univ. Maryland Burke Squires, Influenza Research Database (IRD) / UT Southwestern Ryan Brinkman, BCCRC Richard Scheuermann, IRD / UT Southwestern 1
Influenza Research Database (IRD) www.fludb.org Clinical Data 2
Wild Bird Surveillance Sequence Features 3
Experiment Data Influenza Ontology Domains Host and Pathogen Anatomy Taxonomy Biological Material (specimens) Infectious Disease (disease features & clinical findings) Laboratory Experiment (scientific procedures) Surveillance for transmission and prevalence 4
RELATION TO TIME GRANULARITY CONTINUANT OBO Foundry Map INDEPENDENT DEPENDENT OCCURRENT COMPLEX OF ORGANISMS ORGAN AND ORGANISM CELL AND CELLULAR COMPONENT Family, Community, Deme, Population Organism (NCBI Taxonomy) Cell (CL) Anatomical Entity (FMA, CARO) Cellular Component (FMA, GO) Organ Function (FMP, CPRO) Cellular Function (GO) Population Phenotype Phenotypic Quality (PaTO) Population Process Biological Process (GO) MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Process (GO) http://obofoundry.org 9 Upper level: Basic Formal Ontology (BFO) Continuants Occurrents Qualities (PATO) Information Entities (IAO) Processes CHEBI - chemical entities NCBI taxonomy Other OBO Foundry ontologies Material Entities OBI: samples (blood, urine), cell, instrumentation VO: vaccine parts (pathogen, adjuvant), vaccine, vaccine manufacturer IDO: populations, prion, virion OBI: injection, assays, information processing VO: response to vaccine, vaccine coverage, vaccine rapid implementation IDO: immunization, colonization of host, infection process, transmission of infectious agent IDO: the Infectious disease ontology Available at http://www.infectiousdiseaseontology.org/ VO: the Vaccine Ontology Available at http://www.violinet.org/vaccineontology/ Other OBO Foundry ontologies available at http://www.obofoundry.org/ OBI: the Ontology for Biomedical Investigations Available at http://purl.obofoundry.org/obo/obi PATO: the Phenotypic Quality Ontology Available at http://bioontology.org/wiki/index.php/pato:main_page IAO: the Information Artifact Ontology Available at http://purl.obolibrary.org/obo/iao 5
Example terms from Influenza Ontology Surveillance (Avian) Wild Domestic Migratory / non-migratory Virus Experimental Infection Event Route of delivery 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 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) Completed Compare minimum information for avian surveillance to draft ontology terms Compare draft minimum information for a passage event document February - March, 2010 Complete minimum information for passage experiment comparison Add missing terms from minimum information document to ontology Submit new terms to reference ontology April, 2010 Draft submitted to OBO Foundry ~75 Terms in Version 1 6
Virus Pathogen Database and Analysis Resource (ViPR) www.viprbrc.org Disease Ontology needs Viral encephalitis Viral hemorrhagic fever Viral hepatitis Influenza 7
Influenza Ontology & IDO Influenza ontology is an extension of IDO Additionally, Influenza Ontology covers domains outside of IDO (e. g. surveillance) A disease is a disposition rooted in a physical disorder in the organism and realized in pathological processes. produces bears realized_in etiological process disorder disposition pathological process produces diagnosis interpretive process signs & symptoms abnormal bodily features produces used_in recognized_as 16 8
Influenza - infectious Etiological process - infection of airway epithelial cells with influenza virus produces Disorder - viable cells with influenza virus bears Disposition (disease) - flu realized_in Pathological process - acute inflammation produces Abnormal bodily features recognized_as Symptoms - weakness, dizziness Signs - fever Symptoms & Signs used_in Interpretive process produces Hypothesis - rule out influenza suggests Laboratory tests produces Test results - elevated serum antibody titers used_in Interpretive process produces Result - diagnosis that patient X has a disorder that bears the disease flu 17 9