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Randi Vita, M.D. Ontology Usage by the Immune Epitope Database and Analysis Project La Jolla Institute for Allergy & Immunology Division of Vaccine Discovery La Jolla, California 1 What is an epitope? The portion of a pathogen, allergen, or autoantigen that the immune system recognizes is the epitope Antibodies and T cells bind to epitopes to trigger an immune response 2 Why do epitopes matter? Vaccine development Allergy immunotherapy Immunogenicity Transplantation 3 Antibody Epitopes Antibodies typically bind to discontinuous residues of proteins 4 T cells recognize epitopes (typically peptides) presented by MHC Molecules T cell APC 5 Nonpeptidic Epitopes Antibodies and T cells also bind to lipids, metals, carbohydrates, drugs, etc. Example epitopes: penicillin, nickel, beryllium, cardiolipin, alpha-Galc 6 The Immune Epitope Database Free online resource of experimentally-derived epitope information Scope Allergy Infectious diseases Autoimmune diseases Transplant/alloantigens 7 IEDB Status IEDB has >99% of all published epitope data PubMed is queried every 2 weeks New data is added every week Goal is to have 80% of newly published data publically available within 6 weeks 8 The Immune Epitope Database 17,537 references >1,000,000 assays 214,332 peptidic epitopes 2,379 nonpeptidic epitopes 584 T cell epitopes 1925 Antibody epitopes 9 Data Structure A database of experiments OBI Assay Host Immunization Antibody or T cell Antigen Assay Host Immunization Antibody or T cell Antigen Assay Host Immunization Antibody or T cell Antigen Assay Host Immunization Antibody or T cell Antigen Assay Host Immunization Antibody or T cell Antigen Epitope Reference Epitope Epitope 10 Collaborations with existing resources and ontologies Ensures consistency and accuracy Provides standardized nomenclature Provides definitions, synonyms, and hierarchical relationships for database terms Makes curation easier Enhances user experience Facilitates interoperability 11 Protein Resources Amino acid sequence Peptidic Epitope Protein source Organism source PKYVKQNTLKLAT hemagglutinin HA1 GenBank/UniProt GI:82032767—UniProt:P03452 12 Organism Ontology Amino acid sequence Peptidic Epitope Protein source Organism source Human herpesvirus 5 (HHV-5) NCBI taxon:10359 13 Chemical Ontology Epitope structure Non-peptidic Epitope Epitope source Amoxicillin ChEBI CHEBI:2676 Organism source 14 Disease Ontology Host Immunization Immunogen Process(es) Disease Peanut allergy DO DOID:4378 15 Assay Ontology Assay Type Assay T cells MHC restriction ELISA IL-2 release OBI OBI:1110152 16 MHC Restriction Ontology Assay Type Assay T cells MHC restriction HLA-DPA1*02:01/DPB1*01:01 protein complex MRO MRO_0001175 17 18 Chemical Entities in IEDB Peptidic epitopes Modified peptides Non-peptidic epitopes Diseases caused by chemicals 19 Chemical Entities in IEDB Peptidic epitopes Large amounts of data Described by letters Modified peptides PubChem 20 Chemical Entities in IEDB Non-peptidic epitopes ChEBI Roles 21 Chemical Entities in IEDB Diseases involving chemicals Establish links: Disease Ontology → ChEBI Example: penicillin allergy (DO:XXX) manifests in allergic reaction to penicillin (CHEBI:17334) 22 What the chemical informatics community can do for immunology Immunologist friendly hierarchies Links back to biology Query across resources 23 Organism example in IEDB NCBI hierarchy 24 Organism example in IEDB Immunologist friendly hierarchy 25 Immunologist friendly chemical hierarchy 26 Links back to biology Immunologist groupings without obvious chemical relationships Chlamydiae Lipopolysaccharide ChEBI:16412 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid CHEBI:43577 alpha-D-Kdo-(2->8)-alpha-D-Kdo-(2->4)-alpha-D-Kdo-(2->6)-beta-D-GlcN4P-(1->6)-alpha-D-GlcN-1P ChEBI:61714 Shigella Lipopolysaccharide ChEBI:16412 alpha-L-Rhap-(1->2)-alpha-L-Rhap-(1->3)-[alpha-D-Glcp-(1->4)]-alpha-LRhap-(1->3)-beta-D-GlcpNAc-(1->2)-alpha-L-Rhap3Ac-(1->2)-alpha-LRhap-(1->3)-[alpha-D-Glcp-(1->4)]-alpha-L-Rhap-(1->3)-beta-DGlcpNAc,OCH2CH2NH2 CHEBI:78942 Autoantigens cardiolipin CHEBI:28494 phosphatidylinositol CHEBI:28874 beta-D-Gal-(1->3)-beta-D-GalNAc-(1->4)-beta-D-Gal-(1->4)-beta-D-Glc(1<->1')-Cer CHEBI:27938 27 Query across resources If more resources represent biological / chemical information utilizing formal ontologies (especially OBO foundry) • Interoperability between data sources is faciliated • Queries across resources become possible. Examples: What are shared features of chemicals causing allergic responses 28 Thanks ChEBI Leidos James Overton Evan Bolton IEDB Team 29