Abstract
Easy access to a vast collection of experimental data on immune epitopes can greatly facilitate the development of therapeutics and vaccines. The Immune Epitope Database and Analysis Resource (IEDB) was developed to provide such a resource as a free service to the biomedical research community. The IEDB contains epitope and assay information related to infectious diseases, autoimmune diseases, allergic diseases, and transplant/alloantigens for humans, nonhuman primates, mice, and any other species studied. It contains T cell, B cell, MHC binding, and MHC ligand elution experiments. Its data are curated primarily from the published literature and also include direct submissions from researchers involved in epitope discovery. This article describes the process of capturing data from these sources and how the information is organized in the IEDB data. Different approaches for querying the data are then presented, using the home page search interface and the various specialized search interfaces. Specific examples covering diverse applications of interest are given to highlight the power and functionality of the IEDB.
Highlights
As of November 2016, the Immune Epitope Database and Analysis Resource (IEDB) data were derived from over 18,000 papers
The curation of nonpeptidic structures within the IEDB conforms with the Chemical Entities of Biological Interest (ChEBI) database in the UK [8]
Each Immunome Browser (IB) plot of response frequency scores will automatically include the name if the reference proteome/genome selected for mapping of queried epitope data; the graphical overlay of the individual HCV proteins depicted here was superimposed within the figure as a point of reference and is not an automated feature of the IB
Summary
The Immune Epitope Database (IEDB) is a free online resource that catalogs and makes accessible to the scientific community epitope-related data derived from allergic diseases, infectious diseases, apart from HIV which is captured separately in the Los Alamos HIV database [1], autoimmune diseases, and diseases associated with transplantation and alloantigens. The IEDB contains nearly 300 submissions (corresponding to approximately 20% of the total data) from several NIH-funded large-scale epitope discovery programs and from researchers that directly approach the IEDB to deposit their data, including negative data, which might typically appear in supplemental tables or might not be published at all. Journal of Immunology Research centric design, capturing the experiments (assays) that characterize and define each epitope. This required translation of the data typically described in the methods and results sections of a scientific paper into a generic data structure in which epitope data are entered and stored in a format that allows users to query for the characteristics of these epitopes. We will present a detailed account of the IEDB query and reporting and provide several specific examples
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