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Article
Open AccessPEPMatch: a tool to identify short peptide sequence matches in large sets of proteins
Numerous tools exist for biological sequence comparisons and search. One case of particular interest for immunologists is finding matches for linear peptide T cell epitopes, typically between 8 and 15 residues...
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Protocol
IEDB and CEDAR: Two Sibling Databases to Serve the Global Scientific Community
Various methodologies have been utilized to analyze epitope-specific responses in the context of non-self-antigens, such as those associated with infectious diseases and allergies, and in the context of self-a...
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Article
Open AccessA curated collection of human vaccination response signatures
Recent advances in high-throughput experiments and systems biology approaches have resulted in hundreds of publications identifying “immune signatures”. Unfortunately, these are often described within text, fi...
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Article
Open AccessReporting and connecting cell type names and gating definitions through ontologies
Human immunology studies often rely on the isolation and quantification of cell populations from an input sample based on flow cytometry and related techniques. Such techniques classify cells into populations ...
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Article
Open AccessAn ontology for major histocompatibility restriction
MHC molecules are a highly diverse family of proteins that play a key role in cellular immune recognition. Over time, different techniques and terminologies have been developed to identify the specific type(s)...
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Article
Open AccessQuery enhancement through the practical application of ontology: the IEDB and OBI
Ontologies categorize entities, express relationships between them, and provide standardized definitions. Thus, they can be used to present and enforce the specific relationships between database components. T...
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Chapter
Ontology Development for the Immune Epitope Database
A key challenge in bioinformatics today is ensuring that biological data can be unequivocally communicated between experimentalists and bioinformaticians. Enabling such communication is not trivial, as every s...
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Article
Open AccessCuration of complex, context-dependent immunological data
The Immune Epitope Database and Analysis Resource (IEDB) is dedicated to capturing, housing and analyzing complex immune epitope related data http://www.immuneepitope.org
