Influenza Ontology Infectious Disease Ontology Workshop 2008 Burke Squires.

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Presentation transcript:

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 20 th 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 CollectDefine Relationships HierarchyBFO Links ReferenceApp (IDO) Evaluation TestValidate

Collecting Terms BioHealthBase (98) CEIRS Research (44) CEIRS Surveillance (125) Clinical (19)HEDDS (48) LEMUR (96) MITRE (36) 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 Define terms Divide and conquer Search for terms IDO Reference Organize Link OBO Edit

Rooted in BFO Independent continuant –Primary specimen -> amplified strain specimen, vaccine Dependent continuant –Qualities of above Contexts Event Specification

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

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)

projects/InfluenzO