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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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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.
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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.

Mentions: The Molecule Finder has two top-level branches for peptidic and non-peptidic epitopes. Non-peptidic epitopes are assigned to sources in ChEBI (3) and displayed using the ChEBI hierarchy. Peptidic epitopes derived from proteins occurring in nature have their specific source protein identified by GenPept (5) entries. The variety of distinct sequences represented in GenPept (e.g. the five versions of Phl p I shown in Figure 5) is necessary and reflective of the heterogeneity of proteins within individual species; however, the large number of entries and lack of standardized nomenclature previously overwhelmed users, and made it difficult to obtain all epitopes belonging to a single antigen.


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)

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.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4384014&req=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.
Mentions: The Molecule Finder has two top-level branches for peptidic and non-peptidic epitopes. Non-peptidic epitopes are assigned to sources in ChEBI (3) and displayed using the ChEBI hierarchy. Peptidic epitopes derived from proteins occurring in nature have their specific source protein identified by GenPept (5) entries. The variety of distinct sequences represented in GenPept (e.g. the five versions of Phl p I shown in Figure 5) is necessary and reflective of the heterogeneity of proteins within individual species; however, the large number of entries and lack of standardized nomenclature previously overwhelmed users, and made it difficult to obtain all epitopes belonging to a single antigen.

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
Related in: MedlinePlus