Influenza Ontology

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Influenza Ontology

• Infectious Disease Ontology Workshop 2008
• Burke Squires

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Outline

• Motivation Use case
• Influenza ontology development
• Challenges
• Evaluation
• Joanne Luciano

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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)

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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)

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Influenza Structure

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

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Influenza Life Cycle
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CEIRS Introduction

• Areas of Focus
• Research
• Surveillance
• Genotype-phenotype connection
• Motivation
• Search for assays of virulence
• Support cross-experiment comparison

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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

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CEIRS Use Case
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CEIRS Surveillance Use Case
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Outline

• Motivation use case
• Influenza ontology development
• Challenges
• Evaluation

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Influenza Ontology Development
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Collecting Terms
Gemina (26)
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Consolidated List of Terms

• 200 terms total
• Duplicates removed
• Culled list of database artifacts
• Database permissions
• Final total
• 300 terms (with parents, defined classes)

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Influenza Ontology Development
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Rooted in BFO

• Independent continuant
• Primary specimen -gt amplified strain specimen,
  vaccine
• Dependent continuant
• Qualities of above
• Contexts
• Event
• Specification

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Reference Ontologies
Cell Ontology (CL) Cell types from prokaryotic to mammalian
Common Anatomy Reference Ontology (CARO) Anatomical structures in all organisms
Disease Ontology (DO) Types of human disease (InfluenzO is a subset of this ontology)
Dublin Core (DC) Interoperable online metadata standards
Environment Ontology (EnvO) Habitats and environments of organisms and biological samples
Foundational Model of Anatomy (FMA) Structure of the mammalian and in particular the human body
Gazetteer (GAZ) Geographic location, places and place names and their relationships
Gene Ontology (GO) Attributes of gene products in all organisms
Infectious Disease Ontology (IDO) Relevant to both biomedical and clinical aspects of infectious diseases (InfluenzO is a subset of this ontology)
Ontology for Biomedical Investigations (OBI) Design, protocol, instrumentation and analysis applied in biomedical investigations
Ontology for Clinical Investigations (OCI) Clinical trials and related clinical studies
Pathogen Transmission (TRANS) How a pathogen is transmitted from one host, reservoir, or source to another host
Phenotypic Quality Ontology (PATO) Qualities of biomedical entities
Protein Ontology (PRO) Protein types and modifications classified on the basis of evolutionary relationships
Relation Ontology (RO) Relations in biomedical ontologies
RNA Ontology (RnaO) RNA three-dimensional structures, sequence alignments, and interactions
Sequence Ontology (SO) Features and properties of nucleic acid sequences
Zebrafish Anatomical Ontology (ZAO) Anatomical structures in Danio rerio
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Our current status

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

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InfluenzO
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Assays of Virulence
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Outline

• Motivation use case
• Influenza ontology development
• Challenges
• Evaluation

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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?

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Evaluation
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Acknowledgements

• 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)

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http//sourceforge.org/projects/InfluenzO