Specialized Search Feature (IEDB 3.0)

The Advanced queries are based on a standard Query by Example (QBE) approach, which is a method of forming queries where a user can enter conditions for each data field they want included in the query.  The Specialized queries allow users to define example criteria for each field in the system.  As there are over 300 fields, the Specialized queries are both powerful and comprehensive.

 The fully expanded input screen for the Epitope Details Search is shown in Figure 1.  The user can specify criteria in the left-hand panels for Epitope and Reference.  These sections expand to the right to expose more detailed criteria for the search, including autocomplete fields and finders.  An example of the expanded Epitope box is found in Figure 2.  Users can specify search criteria for the epitope, such as epitope type (e.g. peptide from protein, carbohydrate), source molecule and organism, and various reference details.  Further explanation of the search terms can be found in the Curation Manual.  Using the bottom Reference section, the user can search on several reference criteria, such as author name, article title, the IEDB Reference ID, keywords in the reference abstract, year, author affiliation, and reference type.  References are either published literature articles that have been curated by the IEDB curation staff or data submitted directly by researchers.  This query type returns T cell, B cell, and MHC ligand data.

 Auto-complete functionality is available for all the finder fields, as denoted by the greyed text that provide example inputs.  The “?” provides a brief explanation and a “Learn More” link that connects to the appropriate help page in the IEDB Solutions Center.  Finders are described in further detail in other Help toics.

 Figure 2 shows the fields when “Structure Type - Any” is selected in the Epitope filter.  The fields for the other epitope type selections are shown in Figure 3 (linear epitopes), Figure 4 (Discontinuous epitopes), Figure 5 (Discontinuous peptides on Multichain), and Figure 6 (Non-peptidic epitopes).

 There are four other Specialized queries that can be used to select search criteria for references, epitopes, and assays.  These are T Cell Assay Details, B Cell Assay Details, MHC Assay Details, and Identifier Search.  As an example, the MHC Assay Detailed Search page is shown in Figure 7.  As is the case for all three assay search pages, the Epitope and Reference criteria fields are listed first and last, respectively, with the other relevant filter criteria specific for each assay type listed between them.

 The B cell response assay category captures B cell-mediated immunity information and describes antibody responses related to the epitope/antigen.  In a B cell response, B lymphocytes (a type of white blood cell) produce proteins called antibodies that bind to antigens.  Antibodies are present on the surface on B lymphocytes and are also secreted.  Once an antibody binds an antigen, the bound antigen molecule can be engulfed by phagocytes and broken into fragments. 

 The T Cell Response assay category captures T cell-mediated immunity information where the MHC molecule/antigen complex is recognized by T cells in the context of presentation by an antigen presenting cell.

 The MHC Ligand assay category combines assays that were previously in the MHC Binding and MHC Ligand Elution assay categories.  As such, the MHC Ligand category captures details relating to the in vitro interaction of the epitope with specific MHC molecules along with available Epitope-MHC complex structure details, that is the epitope's binding capacity to the MHC molecule.  It also captures data related to epitopes that are naturally processed and presented on the surface of an antigen presenting cell.  The MHC Ligand Elution subcategory differs from the MHC Binding subcategory in that for the former, antigen bound to the MHC molecule on the cell surface has been taken up and processed internally for presentation by the antigen presenting cell, where as for the latter, antigen in solution is bound to MHC molecules on the surface of the antigen presenting cells.

 The Identifier Search input screen is shown in Figure 8.  If users know the epitope, reference, submission, or assay identifier they are seeking, they can enter that information into one of the four IEDB Identifiers fields.  Users can also look for information based on the PubMed ID of a reference, the PDB ID of a structure, or the ChEBI ID of a nonpeptidic ligand by using the External Identifiers fields.