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)• Centers for Excellence in Influenza Research

and Surveillance (CEIRS)

– Gemina (Lynn Schriml)– MITRE (Bioforensics) (Joanne Luciano)

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)

Influenza Structure

Single stranded, negative sense RNA virus

Segmented genome – 8 segments

11 Proteins Serotype (H5N1)

– Hemagluttanin (16 types)– Neuraminidase (9 types)

Influenza Life Cycle

CEIRS Introduction

Areas of Focus– Research– Surveillance

Genotype-phenotype connection Motivation

– Search for “assays of virulence”– Support cross-experiment comparison

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

CEIRS Use Case

CEIRS Surveillance Use Case

Outline

Motivation & use case Influenza ontology development Challenges

Evaluation

Influenza Ontology Development

Collecting Terms

Gemina (26)

Consolidated List of Terms

200 terms total– Duplicates removed

Culled list of database artifacts– Database permissions

Final total– ~300 terms (with parents, defined classes)

Influenza Ontology Development

Reference Ontologies

Cell Ontology (CL) Cell types from prokaryotic to mammalianCommon 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 standardsEnvironment Ontology (EnvO) Habitats and environments of organisms and biological samples

Foundational Model of Anatomy (FMA) Structure of the mammalian and in particular the human bodyGazetteer (GAZ) Geographic location, places and place names and their relationshipsGene 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 sequencesZebrafish Anatomical Ontology (ZAO) Anatomical structures in Danio rerio

Our current status

Basic structure in place Adding final definitions Checking each term for reference

ontology link Preparing first draft release Dec. 1

InfluenzO

Assays of Virulence

Outline

Motivation & use case Influenza ontology development Challenges

Evaluation

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?

Evaluation

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)

http://sourceforge.org/projects/InfluenzO