Transcript Influenza Ontology - Buffalo Ontology Site

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
Terms
Collect
Define
Relationships
Hierarchy
BFO
Links
Reference
App (IDO)
Evaluation
Test
Validate
Collecting Terms
BioHealthBase
(98)
CEIRS
Research
(44)
MITRE (36)
CEIRS
Surveillance
(125)
LEMUR (96)
HEDDS (48)
Clinical (19)
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
Organize
Define terms
• Link
• OBO Edit
• Divide and
conquer
Search
for terms
• IDO
• Reference
Reference Ontologies
Cell Ontology (CL)
Common Anatomy Reference Ontology (CARO)
Cell types from prokaryotic to mammalian
Anatomical structures in all organisms
Disease Ontology (DO)
Dublin Core (DC)
Environment Ontology (EnvO)
Foundational Model of Anatomy (FMA)
Gazetteer (GAZ)
Gene Ontology (GO)
Pathogen Transmission (TRANS)
Phenotypic Quality Ontology (PATO)
Types of human disease (InfluenzO is a subset of this ontology)
Interoperable online metadata standards
Habitats and environments of organisms and biological samples
Structure of the mammalian and in particular the human body
Geographic location, places and place names and their relationships
Attributes of gene products in all organisms
Relevant to both biomedical and clinical aspects of infectious diseases
(InfluenzO is a subset of this ontology)
Design, protocol, instrumentation and analysis applied in biomedical
investigations
Clinical trials and related clinical studies
How a pathogen is transmitted from one host, reservoir, or source to
another host
Qualities of biomedical entities
Protein Ontology (PRO)
Relation Ontology (RO)
Protein types and modifications classified on the basis of evolutionary
relationships
Relations in biomedical ontologies
RNA Ontology (RnaO)
RNA three-dimensional structures, sequence alignments, and
interactions
Sequence Ontology (SO)
Zebrafish Anatomical Ontology (ZAO)
Features and properties of nucleic acid sequences
Anatomical structures in Danio rerio
Infectious Disease Ontology (IDO)
Ontology for Biomedical Investigations (OBI)
Ontology for Clinical Investigations (OCI)
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