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. 2015 Jan;43(Database issue):D405-12.
doi: 10.1093/nar/gku938. Epub 2014 Oct 9.

The immune epitope database (IEDB) 3.0

Randi Vita  1 , James A Overton  2 , Jason A Greenbaum  3 , Julia Ponomarenko  4 , Jason D Clark  5 , Jason R Cantrell  5 , Daniel K Wheeler  5 , Joseph L Gabbard  6 , Deborah Hix  6 , Alessandro Sette  2 , Bjoern Peters  2
Affiliations

The immune epitope database (IEDB) 3.0

Randi Vita et al. Nucleic Acids Res. 2015 Jan.

Abstract

The IEDB, www.iedb.org, contains information on immune epitopes--the molecular targets of adaptive immune responses--curated from the published literature and submitted by National Institutes of Health funded epitope discovery efforts. From 2004 to 2012 the IEDB curation of journal articles published since 1960 has caught up to the present day, with >95% of relevant published literature manually curated amounting to more than 15,000 journal articles and more than 704,000 experiments to date. The revised curation target since 2012 has been to make recent research findings quickly available in the IEDB and thereby ensure that it continues to be an up-to-date resource. Having gathered a comprehensive dataset in the IEDB, a complete redesign of the query and reporting interface has been performed in the IEDB 3.0 release to improve how end users can access this information in an intuitive and biologically accurate manner. We here present this most recent release of the IEDB and describe the user testing procedures as well as the use of external ontologies that have enabled it.

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Figures

Figure 1.
Figure 1.
(A) The distribution of data in the IEDB by scientific field. (B) Curation of relevant references over time.
Figure 2.
Figure 2.
The IEDB 3.0 home page has the most commonly used search parameters centered on the page, shown in box (A), with the highly used analysis tools made more prominent, shown in box (B).
Figure 3.
Figure 3.
New results presentation format shows current search filters in box (A), counts returned per data type in box (B) and the new left search panel allowing for continued refinement or editing of one's query, such as by the epitope source, in box (C).
Figure 4.
Figure 4.
Comparison of classifications of pairs between NCBI Taxonomy and IEDB organism tree. Left: correct classifications. Right: uncertain classifications. The Wilcoxon signed rank test shows that both results are statistically significant with a P-value of <0.0001.
Figure 5.
Figure 5.
The Molecule Finder provides a hierarchical organization of proteins that allows narrowing the search to epitopes derived from a specific antigen, such as the common allergen Phl p 1. The reference proteome protein ‘Phl p 1’ is the parent of five individual GenPept entries for this protein from Timothy grass.
Figure 6.
Figure 6.
Immunome Browser plots for the epitopes from the Timothy grass allergen Phl p 1 recognized in the human T cell response.
See this image and copyright information in PMC

References

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