The results of a search or query appear on the Results page (http://www.iedb.org/result_v3). An example is shown in Figure 1. The search criteria are listed in the Current Filters section above the results table. There are four tabs for the results. Figure 1 displays the Epitopes tab. Results are initially sorted by the number of assays, but the user can click on the column header to change the sort order. A second click will reverse the sort order of the selected column. The table includes the epitope structure description, the corresponding antigen, source organism, the number of references in which the epitope appears, and the number of assays (positive and negative) that reside in the database. Clicking on the Epitope ID number in the far left column will take the user to a Distinct Epitope detail page, as seen in Figure 2. The bottom section of the figure contains links to relevant tools in the Analysis Resource. Links can also appear to the Bioinformatics Resource Centers (BRC), such as the Influenza Research Database (IRD). The user can also refine the search results by clicking on the filter icon in the epitope, antigen, and organism fields.
Figure 1. The Epitope tab of the search results page
Figure 2. An example of the epitope detail page
The second tab on the results page is the Antigens tab (Figure 3). Results are initially sorted by the number of assays, but the user can click on the column header to change the sort order. The table includes the antigen name, the corresponding source organism, the number of associated antigen epitopes in the IEDB, and the number of assays (positive and negative) that reside in the database. The user can explore the data related to a particular antigen by clicking on the funnel icon in the righthand side of the Antigen column. The data in the other three tabs will change accordingly as seen in Figure 4.
Figure 3. The Antigens tab of the search results page
Figure 4. The Results filtered by the Nucleoprotein of the Influenza A virus. This was achieved by clicking on the filter icon in the antigen column. The content of the other tabs contain data specific to this antigen.
The third tab on the results page is the Assays tab (Figure 5). Results are initially sorted by the Assay Description, but the user can click on the column header to change the sort order. The table contains three additional tabs, one each for the three assay categories – T cell, B cell, and MHC Ligand. The table for the T cell assays includes the assay ID, the reference, epitope, host organism, immunization, assay antigen, antigen epitope relation, MHC restriction, and assay description. The content of the B cell assay tab is the same except it omits the MHC restriction column. The MHC ligand assay tab contains fields for assay ID, reference, epitope, antigen processing, MHC restriction, assay description, and quantitative measure. Clicking on the Assay ID in the far left lane will take the user to an Assay Detail page. An example is given in Figure 6. The actual page contains additional fields below what is shown in the figure. The user can also refine the results further by clicking on the filter icon that is available in several of the fields, such as reference, epitope, and host.
Figure 5. The Assays tab of the search results page. The page contains three additional tabs for T Cell, B Cell, and MHC Ligand Assays
Figure 6. The top three sections of a sample T cell assay detail page
The fourth tab on the results page is the References tab (Figure 7). Results are initially sorted by the year of publication or submission, the most recent references first. Again, the user can click on the column header to change the sort order. The table includes the IEDB-assigned reference ID, the PubMed ID, authors, article title, abstract, and the date. For journal articles, the information is downloaded directly from PubMed. Clicking on the Ref ID in the far left lane will take the user to a Reference Detail page. An example is given in Figure 8.
Figure 7. The References tab of the search results page
Figure 8. An example of the Reference detail page
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