The immune epitope database 2.0

Abstract

The Immune Epitope Database (IEDB, www.iedb.org) provides a catalog of experimentally characterized B and T cell epitopes, as well as data on Major Histocompatibility Complex (MHC) binding and MHC ligand elution experiments. The database represents the molecular structures recognized by adaptive immune receptors and the experimental contexts in which these molecules were determined to be immune epitopes. Epitopes recognized in humans, nonhuman primates, rodents, pigs, cats and all other tested species are included. Both positive and negative experimental results are captured. Over the course of 4 years, the data from 180,978 experiments were curated manually from the literature, which covers approximately 99% of all publicly available information on peptide epitopes mapped in infectious agents (excluding HIV) and 93% of those mapped in allergens. In addition, data that would otherwise be unavailable to the public from 129,186 experiments were submitted directly by investigators. The curation of epitopes related to autoimmunity is expected to be completed by the end of 2010. The database can be queried by epitope structure, source organism, MHC restriction, assay type or host organism, among other criteria. The database structure, as well as its querying, browsing and reporting interfaces, was completely redesigned for the IEDB 2.0 release, which became publicly available in early 2009.

Figure 1.

IEDB database architecture diagram. Data are transferred between curation databases via custom PL/SQL procedures. Data are migrated to the data warehouses via SQL and PL/SQL scripts in conjunction with an extract, transform and load (ETL) application.

Figure 2.

Objects, processes and roles as represented in the IEDB.

Figure 3.

Home page search. The search fields are organized into those describing the epitope structure and source (A–D) and the immune recognition context (E–H).

Figure 4.

Host organism search. After entering the common name of ‘mouse’, the Organism Finder returns the scientific name of Mus musculus. The user can decide to select any higher level of the taxonomical tree, such as Rodentia (the synonym list is displayed when mousing over) or can further refine the search by selecting a specific strain.

Figure 5.

The advanced T cell search page. Field groups are collapsed for simplicity and can be opened or collapsed by clicking the + or − sign at each header.