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. 2017;2017:5974574.
doi: 10.1155/2017/5974574. Epub 2017 May 29.

The Immune Epitope Database: How Data Are Entered and Retrieved

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Free PMC article

The Immune Epitope Database: How Data Are Entered and Retrieved

Ward Fleri et al. J Immunol Res. .
Free PMC article

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.

Figures

Figure 1
Figure 1
The Molecule Finder can be used to select the source antigen of the epitope. The yellow highlight icon in the bottom table highlights the selection in the tree in the upper right. The green “+” icon selects the molecule for the search criteria. The stars next to the molecule name indicate the quality and completeness of the associated reference proteome.
Figure 2
Figure 2
The IEDB home page features a search interface in the center of the page.
Figure 3
Figure 3
The Organism Finder can be used to select the search criteria for the epitope source organism. A similar finder is available for selecting the host organism.
Figure 4
Figure 4
The Immunome Browser maps response frequencies and assay counts onto a reference antigen. The polyprotein for HCV is superimposed on the plots for reference. The data reflects IEDB HCV content as of October 2016.
Figure 5
Figure 5
The Immunome Browser generates a table that lists all epitopes and corresponding response information sorted by their mapped position. This table can be downloaded in a CSV-formatted file by clicking on the “Export Results” link in the upper right corner.
Figure 6
Figure 6
The results for a home page query for the linear sequence ASNENMETM, a well-characterized epitope of influenza A virus nucleoprotein. The results include four epitopes with posttranslational modifications.

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