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The immune epitope database (IEDB) 3.0.

Vita R, Overton JA, Greenbaum JA, Ponomarenko J, Clark JD, Cantrell JR, Wheeler DK, Gabbard JL, Hix D, Sette A, Peters B - Nucleic Acids Res. (2014)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, 9420 Athena Circle, CA 92037, USA rvita@liai.org.

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Immunome Browser plots for the epitopes from the Timothy grass allergen Phl p 1 recognized in the human T cell response.
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Related In: Results  -  Collection

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Figure 6: Immunome Browser plots for the epitopes from the Timothy grass allergen Phl p 1 recognized in the human T cell response.

Mentions: The improvements made to the Molecule Finder benefit the Immunome Browser, which can utilize the reference proteomes as mapping targets. Previously available as an on-demand visualization tool in the IEDB (10), the Immunome Browser has now been tightly integrated within the antigen tab, redesigned and enhanced based on user feedback. Conceptually, the Immunome Browser is the first analytical tool integrated into the IEDB database, as it does not simply display information as stored in the database, but maps epitopes onto a reference antigen. Similar to the now commonly used genome browsers, this allows for the aggregation of information derived from different sources and their display in a common reference. On the antigen tab, the Immunome Browser can now be used to immediately visualize linear peptidic epitopes retrieved by a query along the length of the parent antigen based on sequence similarity. This displays how often each protein region has been studied in immune assays and in how many assays the immune response was positive or negative. Figure 6 shows the Immunome Browser output for the epitopes from the Timothy grass allergen Phl p 1 recognized in the human T cell response. The upper plot renders the lower and upper bounds of the 95% confidence interval of the response frequency for each target protein position, averaged over all epitopes mapped to that position and calculated as the number of positively responded subjects (or individuals in this case) relative to the total number of those tested. The bottom plot shows the number of positive and negative assays averaged over epitopes mapped to each position in the protein sequence. A table below the graphs (not shown) presents results for each epitope and each protein position in a tabular format that can be saved, along with the graph images, for further analysis and publication. The user can interactively zoom in and out the plots to a specific protein region and the table will update accordingly.


The immune epitope database (IEDB) 3.0.

Vita R, Overton JA, Greenbaum JA, Ponomarenko J, Clark JD, Cantrell JR, Wheeler DK, Gabbard JL, Hix D, Sette A, Peters B - Nucleic Acids Res. (2014)

Immunome Browser plots for the epitopes from the Timothy grass allergen Phl p 1 recognized in the human T cell response.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4384014&req=5

Figure 6: Immunome Browser plots for the epitopes from the Timothy grass allergen Phl p 1 recognized in the human T cell response.
Mentions: The improvements made to the Molecule Finder benefit the Immunome Browser, which can utilize the reference proteomes as mapping targets. Previously available as an on-demand visualization tool in the IEDB (10), the Immunome Browser has now been tightly integrated within the antigen tab, redesigned and enhanced based on user feedback. Conceptually, the Immunome Browser is the first analytical tool integrated into the IEDB database, as it does not simply display information as stored in the database, but maps epitopes onto a reference antigen. Similar to the now commonly used genome browsers, this allows for the aggregation of information derived from different sources and their display in a common reference. On the antigen tab, the Immunome Browser can now be used to immediately visualize linear peptidic epitopes retrieved by a query along the length of the parent antigen based on sequence similarity. This displays how often each protein region has been studied in immune assays and in how many assays the immune response was positive or negative. Figure 6 shows the Immunome Browser output for the epitopes from the Timothy grass allergen Phl p 1 recognized in the human T cell response. The upper plot renders the lower and upper bounds of the 95% confidence interval of the response frequency for each target protein position, averaged over all epitopes mapped to that position and calculated as the number of positively responded subjects (or individuals in this case) relative to the total number of those tested. The bottom plot shows the number of positive and negative assays averaged over epitopes mapped to each position in the protein sequence. A table below the graphs (not shown) presents results for each epitope and each protein position in a tabular format that can be saved, along with the graph images, for further analysis and publication. The user can interactively zoom in and out the plots to a specific protein region and the table will update accordingly.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, 9420 Athena Circle, CA 92037, USA rvita@liai.org.

Show MeSH