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The Immune Epitope Database (IEDB)

NAR Molecular Biology Database Collection entry number 779
Vita, R.1*, Zarebski, L.1, Greenbaum, J.A.1, Emami, H.2, Hoof, I.3, Salimi, N.1, Damle, R.1, Sette, A.1, and Peters, B.1
1The La Jolla Institute for Allergy and Immunology, Center for Infectious Disease; Allergy and Asthma Research La Jolla, California 92037, US
2Science Applications International Corporation, San Diego, California 92121, US
3Center for Biological Sequence Analysis, Department of Systems Biology Technical University of Denmark 2800 Lyngby, Denmark

Database Description

The Immune Epitope Database (IEDB,, provides a catalog of experimentally characterized B and T cell epitopes, as well as data on 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, non-human primates, rodents, pigs, cats and all other tested species are included. Both positive and negative experimental results are captured. Over the course of four years, the data from 180,978 experiments were curated manually from the literature, covering about 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.

Recent Developments

The IEDB recently underwent a major review resulting in significant advancements. Driven by user feedback, curator experience, and the development of the Ontology of Immune Epitopes (ONTIE) [1], data quality was scrutinized and the database schema was redesigned to accommodate new data types and features. The redesigned data schema allowed implementation of formal validation rules, leading to the identification and correction of validation inconsistencies. This process has resulted in drastically improved data consistency. These changes also resulted in enhanced usability for the end users and heightened the potential for future improvements.


1. Vita, R., Vaughan, K., Zarebski, L., Salimi, N., Fleri, W., Grey, H., Sathiamurthy, M., Mokili, J., Bui, H.H., Bourne, P.E., Ponomarenko, J., de Castro, R. Jr., Chan, R.K., Sidney, J., Wilson, S.S., Stewart, S., Way, S., Peters, B., Sette, A. (2006) Curation of complex, context-dependent immunological data. BMC Bioinformatics 7, 341
2. Peters, B., Sidney, J., Bourne, P., Bui, H.H., Buus, S., Doh, G., Fleri, W., Kronenberg, M., Kubo, R., Lund, O., Nemazee, D., Ponomarenko, J.V., Sathiamurthy, M., Schoenberger, S., Stewart, S., Surko, P., Way, S., Wilson, S., and Sette, A. (2005) The Immune Epitope Database and Analysis Resource: from Vision to Blueprint. PLoS Biol. 3(3), e91

Go to the abstract in the NAR 2010 Database Issue.
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