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Nucleic Acids Research Advance Access published online on November 11, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp1004
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

The Immune Epitope Database 2.0

Randi Vita1,*, Laura Zarebski1, Jason A. Greenbaum1, Hussein Emami2, Ilka Hoof3, Nima Salimi1, Rohini Damle1, Alessandro Sette1 and Bjoern Peters1

1La Jolla Institute for Allergy and Immunology, Center For Infectious Disease, Allergy and Asthma Research, 9420 Athena Circle, La Jolla, CA 92037, 2Science Applications International Corporation, IEDB, San Diego, CA, USA and 3Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark

*To whom correspondence should be addressed. Tel: +1 858 752 6912; Fax: +1 858 752 6987; Email: rvita{at}liai.org

Received September 13, 2009. Revised October 15, 2009. Accepted October 16, 2009.

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 ~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.


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