The Immune Epitope Database - Representing Experiments Using the Ontology of Biomedical...

The Immune Epitope Database - Representing Experiments Using the Ontology of Biomedical

Investigations

Bjoern Peters, La Jolla Institute for

Allergy and Immunology10/21/2011, UCSD

Presentation Overview

1. The Ontology of Biomedical Investigations (OBI)

2. The Immune Epitope Database (IEDB) 3. Representing IEDB experiments using OBI4. Flow cytometry in OBI

OBI – a user driven project

• 19 communities that recognized they were trying to solve the same / related problems

• Members typically have one or more applications that drive OBI development

• 6 year effort, 1+ phone calls per week, 1-2 meetings per year

• first stable release (Philly / 1.0) in Oct. 2009 Open project with constant addition of new

communities, please consider joining!

High level class hierarchy (partial)

OBI – Recent Development

• eagle-i project has/is integrating large vocabulary of research resources into OBI

• Evidence Ontology (ECO) codes are being mapped 1:1 to OBI classes to allow ‘round-tripping’ between simple codes (‘direct assay evidence’) and expressive OWL

• Finalization of OBI-core:– Subset of OBI with extra promises for stability and quality– Education tool for both users (where to look) and

developers (where to add stuff)

OBI inner core• planned process – investigation– study design execution– acquisition– specimen collection– human subject enrollment– material transformation– assay– data transformation– documenting

• information content entity– document– study design– hypothesis textual entity– protocol– independent variable specification– dependent variable specification– measurement datum– data item– conclusion textual entity

• dependent continuant– measure function– investigation agent role– study subject role– specimen role

• material entity– device– population– specimen

OBI outer core• biological_process from the Gene Ontology (GO)• cell from the Cell Ontology (CL)• cellular_component from the Gene Ontology (GO)• environmental material from the Environment Ontology (EnVO)• geographical location from Gazetteer• gross anatomical part from the Common Anatomy Reference Ontology (CARO)• Homo sapiens from the National Center for Biotechnology Information Taxonomy

(NCBITaxon)• measurement unit label, included to connect to the Ontology of Units of Measurement (UO)• molecular entity from Chemical Entities of Biological Interest (ChEBI)• organism, included to connect to the

National Center for Biotechnology Information Taxonomy (NCBITaxon)• quality, included to connect to the Phenotypic Quality Ontology (PATO)The following two terms are not in OBI yet:• disease course from the Ontology for General Medical Science (OGMS)• molecular_function from the Gene Ontology (GO)

Immune Epitope Definition

An immune epitope is a part of a moleculethat is directly recognized by

adaptive immune receptors, specifically by antibodies, B cell receptors, or T cell receptors

CD8+ T cell epitopes in viral infection

T Cytokine Release

Cytotoxicity

Proliferation

Virus TCR CD8

ORF 1 M G Q I V T M F E A L P H I I D E V I N I V I I V L I V I T G I K A V Y N ...

ORF 2 M G L K G P D I Y K G V Y Q F K S V E F D M S H L N L T M P N A C S A N N ...

ORF 3 M H N F C N L T S A F N K K T F D H T L M S I V S S L H L S I D G N S N Y ...

ORF 4 M S A Q S Q C R T F R G R V L D M F R T A F G G K Y M R S G W G W T G S D ...

ORF 5 M H C T Y A G P F G M S R I L L S Q E K T K F F T R R L A G T F T W T L S ...

ORF 6 M K C F G N T A V A K C N V N H D A E F C D M L R L I D Y N K A A L S K F ...

ORF 7 M L M R N H L L D L M G V P Y C N Y S K F W Y L E H A K T G E T S V P K C ...

ORF 8 M N M I T E M L R K D Y I K R Q G S T P L A L M D L L M F S T S A Y L V S ...

ORF 9 M S L S K E V K S F Q W T Q A L R R E L Q S F T S D V K A A V I K D A T N ...

T cell epitope mapping