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)

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

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

Mouse

Virus

APC

CD8+ T cell epitopes in viral infection

MHC-I

APC

MHC-I

T Cytokine Release

Cytotoxicity

TT

Proliferation

Mouse

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

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

CD8+ T cell epitopes in viral infection

Goals of the Immune Epitope Database and Analysis Resource (IEDB)

• To catalog, organize and make accessible immune epitope related information– B and T cell epitopes, MHC binding, MHC ligand elution– Scope: infectious diseases, allergy, autoimmunity ,

transplantation. (HIV LANL database; no cancer)• Develop new methods to predict and model immune

responses ( IEDB Analysis Resource)

www.iedb.org

Name 74AChemical Type Peptide/ProteinSequence CLTEYILWVDomain / Region Defined EpitopeSpecies Vaccinia virus AnkaraStrain Ankara (MVA)Antigen putative 21.7k proteinAntigen Accession 2772819Antigen Positions 79-87Immunized Species Homo sapiensImmunogen Type Source SpeciesAdministration ScarificationAntigen Type EpitopeAssay Type ELISPOTResponse Measured Cytokine Release-IFN-gMHC Allele HLA-A*0201

Epitope

Structure

Source

Context

Immunization

Assay

IEDBwww.iedb.org

Literature curationEpitope discovery contract submission

Populating the IEDBPart III: Data representationPart II: Document

categorization

Literature Curation Status

 Category#Relevant

articlesPercent

completedInfectious disease 10,260 99.5%Allergy 1,639 99.1%Autoimmunity 5,160 99.1%Transplant 977 99.3%Total 18,036 99.3%

>99% in all categories since 2011

IEDB applications

Meta-Analyses

Prediction tool development

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

Using OBI to represent experiments in the IEDB

epitope mapping experiments

T

APC

T Cell Response

T B

B Cell Response

journal article

reference (document)

B cell response

has part

High level database structure

is about

T cell response

author submission

epitope structure(material

entity)

peptide

discontinuous protein residues

carbohydrate

epitope source

(material entity)

organism

protein

protein complex

immune recognition

assay (process) MHC binding

has participant

Natural Infection

Administered Immunization

immunization (process)

preceded by

Replacing IEDB controlled vocabularies with OBI classes

• Benefits:– Increase consistency in data curation– Avoid duplicates– Improve documentation to external users– Enhance search capabilities

Original approach: controlled vocabularies• Used existing external ontologies as source where possible

(none available for epitope specific T cell assays) • Maintain list of assays; if a publication uses an assay that is

different, add to this list 140 T cell assays• Challenges :

– Ensure curators pick the right assays– Communicate to external users what each assay is– Avoid introducing duplicates (“MCP-1 IFA” = “CCL-2 histostain”)

• In addition we want to – Search for groups of related assays– Interoperability (lots of it)

Create an OBI class for each entry in our list of assay types

OBI hierarchy

Assay definition: A planned process with the objective to produce information about an evaluant

OWL (partial):has_specified_input some (material_entity and (has_role some 'evaluant role'))

has_specified_output some ('information content entity' and ('is about' some (continuant and (has_role some 'evaluant role'))))

T cell epitope assay design pattern• Majority of assays could be defined with N&S conditions after

specifying two variables: <parent assay type> and has_specified_output some 'measurement datum‘ and 'is about' some (<GO process Y> and 'process is result of' some 'MHC:epitope complex binding to TCR')

• For example: “IL-17 ELISPOT” in the IEDB is logically defined as= 'ELISPOT assay‘ and has_specified_output some

'measurement datum‘ and 'is about' some (‘IL-17 production’ and process is result of' some 'MHC:epitope complex binding to TCR')

• Required expanding parent assay types (OBI) and GO process

Adding parent assay types to OBI• label: cytometric bead array assay• definition: An assay in which a series of beads coated with

antibodies specific for different analytes and marked with discrete fluorescent labels are used to simultaneously capture and quantitate soluble analytes using flow cytometric analysis.

• alternative term: multiplexed bead assay, CBA assay• example of usage: Using a Luminex machine to detect IFN-

gamma and IL-10 in the supernatant of a cell culture “Parent” assay definitions are discussed in OBI as a group and

derived by consensus, to ensure exactness and ability to re-use. Child terms that follow design patterns are added without

group discussion

Modifying external ontologies• Requests for new / modified terms are made through their

respective trackers (sometimes additional prodding is needed)

• Often results in email discussions that clarify issues and result in improved definitions (but take time)

• Succeeded with GO, ChEBI, PRO, OGMS, IDO, PATO, UO, …• Resulting terms are imported into OBI to reference them in

logical definitions (Using MIREOT mechanism)

• Some terms have no ‘natural home ontology’, and are kept in OBI until they can be moved

Mapping IEDB assay types to OBI classesIEDB Assay ID

OBI ID rdfs:label is about biological process (epitope specific T cell response)

assay type (technique)

198 OBI_0000891 assay of epitope specific T cell proliferation epitope specific T cell proliferation assay52 OBI_0001194 ELISPOT assay of epitope specific transforming

growth factor-beta production by T cellsepitope specific transforming growth factor-beta production by T cells

ELISPOT assay

61 OBI_0001196 cytometric bead array assay of epitope specific IP-10 production by T cells

epitope specific IP-10 production by T cells cytometric bead array assay

62 OBI_0001198 assay of epitope specific interleukin-27 production by T cells

epitope specific interleukin-27 production by T cells

assay

64 OBI_0001203 detection of specific nucleic acids with complementary probes of epitope specific transforming growth factor-beta production by T cells

epitope specific transforming growth factor-beta production by T cells

detection of specific nucleic acids with complementary probes

65 OBI_0001206 ELISPOT assay of epitope specific granulocyte macrophage colony-stimulating factor production by T cells

epitope specific granulocyte macrophage colony-stimulating factor production by T cells

ELISPOT assay

66 OBI_0001209 assay of epitope specific interleukin-10 production by T cells

epitope specific interleukin-10 production by T cells

assay

84 OBI_0001210 cytometric bead array assay of epitope specific transforming growth factor-beta production by T cells

epitope specific transforming growth factor-beta production by T cells

cytometric bead array assay

143 OBI_0001215 intracellular cytokine staining assay of epitope specific cytotoxic T cell degranulation

epitope specific cytotoxic T cell degranulation intracellular cytokine staining assay

153 OBI_0001216 cell culture analyte detection bioassay of epitope specific interleukin-2 production by T cells

epitope specific interleukin-2 production by T cells

cell culture analyte detection bioassay

154 OBI_0001217 assay of epitope specific interleukin-22 production by T cells

epitope specific interleukin-22 production by T cells

assay

171 OBI_0001218 assay of epitope specific interleukin-8 production by T cells

epitope specific interleukin-8 production by T cells

assay

174 OBI_0001220 cell culture analyte detection bioassay of epitope specific interleukin-10 production by T cells

epitope specific interleukin-10 production by T cells

cell culture analyte detection bioassay

194 OBI_0001222 ELISA of epitope specific RANTES production by T cells

epitope specific RANTES production by T cells

ELISA

196 OBI_0001223 cytometric bead array assay of epitope specific interleukin-1 beta production by T cells

epitope specific interleukin-1 beta production by T cells

cytometric bead array assay

224 OBI_0001227 ELISPOT assay of epitope specific interleukin-6 production by T cells

epitope specific interleukin-6 production by T cells

ELISPOT assay

254 OBI_0001228 assay of epitope specific T cell enhancement of B cell mediated immune response

epitope specific T cell enhancement of B cell mediated immune response

assay

Spreadsheet based template

Benefits of using OBI classes for IEDB assay types internally

• Formal definitions of assay types serve as curation rules• Issues arising in curation are reflected 1:1 by issues in

writing definitions• Linking to GO identified duplicate assay types

(introduced in the IEDB controlled vocabulary as a result of changes in nomenclature over time)

The same could have been achieved by carefully writing definitions for our controlled vocabulary terms, but ontologies can do more…

Reasoning introduces hierarchy

Display with community specific“IEDB alternative label”

Assay type ID [Primary Key]

Assay type name

Ontology ID[could be more than just OBI]

1 IFN-g ELISPOT http://purl.obolibrary.org/obo/OBI_00014142 Survival http://purl.obolibrary.org/obo/OBI_00013343 IL-10 FACS http://purl.obolibrary.org/obo/OBI_00004144 DTH http://purl.obolibrary.org/obo/OBI_0002114 … … …

Benefits of using OBI for external users

Required (minimal) modification of the assay type table

This allowed us to use OBI

Ontology driven search interface

• Search for groups of related assays• Search using synonyms•Use IEDB specific labels

Future work

• Export IEDB data into triple store, enabling Sparql queries seamless interoperability

• Integration into rule based validation system

Overall Conclusions

• The IEDB catalogs and organizes experimental data characterizing immune epitopes

• We implemented a machine learning pipeline to identify and triage journal articles relevant for subject areas of interest

• OBI provides a framework to represent experimental information in an interoperable and semantically rich format that has immediate benefits for database resources such as the IEDB

Flow cytometry for IEDB• IL-10 production (GO)• Epitope specific IL-10 production by T cells (OBI helper

term).– Textual Definition: “A biological process where T cells produce

IL-10 resulting from the recognition of a T cell epitope”– Logical definition:

“'interleukin-10 production‘ and ('process is result of' some 'MHC:epitope complex binding to TCR')”

• Intracellular cytokine staining assay (OBI)• T cell epitope intracellular cytokine staining IL-10 assay

(OBI, term that really just the IEDB wants) Tie to cells, cell populations

Immunology terms in OBI• There is no ‘immune epitope ontology’ merged into OBI

• These terms are looking for a new home: – disposition to be bound by immune receptor– binding– Epitope, antigen, immunogen, allergen, host– ‘epitope specific cytokine production by T cells’– Environmental exposure / proximity to infectious agent (IDO)

Thanks!SAIC• Stephen Greenlee• Jason Cantrell• Jason Buell• Robert Hinman• Kelly Wheeler• Eric Gutt

San Diego Supercomputer Center

• Phil Bourne• Julia Ponomarenko

Technical University of Denmark• Ole Lund• Morten Nielsen

University of Copenhagen• Søren Buus

La Jolla Institute for Allergy & Immunology