The Immune Epitope Database (IEDB): 2024 update

Abstract

Over the past 20 years, the Immune Epitope Database (IEDB, iedb.org) has established itself as the foremost resource for immune epitope data. The IEDB catalogs published epitopes and their contextual experimental data in a freely searchable public resource. The IEDB team manually curates data from the literature into a structured format and spans infectious, allergic, autoimmune, and transplant diseases. Here, we describe the enhancements made since our 2018 paper, capturing user-directed updates to the search interface, advanced data exports, increases in data quality, and improved interoperability across related resources. As we look forward to the next 20 years, we are confident in our ability to meet the needs of our users and to contribute to the broader field of data standardization.

Graphical Abstract

Figure 1.

Data growth. Here, we present an overview of how the content of the IEDB has changed between the end of 2010, the first year that we were fully up to date with the literature, the end of 2018, when we last published a review on the IEDB, and current day. (A) The most growth has been noted in the numbers of assays per epitope and per publication. (B) MHC ligand assays have increased more rapidly than either B cell or T cell assays, as MHC ligand elution publications tend to elute thousands of epitopes per a single publication.

Figure 2.

Filter options. These options convert the generic query interface into three specialized views with additional, community-relevant search parameters. The ‘?’ icon takes users to a short video and a detailed help article describing this new feature. (A) T cell options include parameters relevant to T cell researchers such as TCR, direct ex vivo analysis, and MHC details. (B) B cell filter options include antibody/BCR, isotype, and B cell specific assay types. (C) MHC options include MHC assay types and MHC molecule details such as resolution and evidence.

Figure 3.

Protein tree. The Protein Tree allows us to present a vast amount of data in a simplified way. (A) Queries on specific fragments of a protein are enabled. (B) Synonyms imported from UniProt allow users to search by common names. (C) IUIS official nomenclature is used to present allergens.

Figure 4.

Antigen Summary page. This new page presents all information in the IEDB for any given antigen and also includes links to other resources. (A) The summary presents synonyms, counts of epitopes, publications, assays, 3D structures, and contextual information such as the hosts and disease states in which it was tested. (B) The compiled data for each protein, which is divided between linear and discontinuous epitopes, and shows how many of each had assays with positive outcomes versus how many assays were performed. (C) At the bottom of each Antigen Summary page, links out to other overlapping resources will be provided. We intend to add to this section over time, as new contacts are made.

Figure 5.

3D viewers. Three custom viewer applications are tailored for specific aspects of epitope visualization. (A) Experimentally-determined 3D structures of MHC-,TCR- or BCR-related complexes are accessible through the Assays tab. (B) Epitopes can be viewed in the context of the 3D structure or 3D model of the antigen through the Epitopes tab. (C) Immunogenicity regions on the antigen can be viewed through the ImmunomeBrowser tool.

Figure 6.

New export features. (A) Each tab of results can be exported via the ‘Export Results’ icon. (B) Exports are now available in a variety of file formats and users can select which columns of the data that they want to export. A ‘?’ icon takes users to a detailed help article describing the export features (C). Exports now include the query parameters and a help tab.