How do I generate data for all epitopes that have been associated with in vitro correlates of protection (virus neutralization, CTL, inhibition of infectivity, etc.)? Can I search by the type of assay?
On the 'Search' pull-down tab along the top on the IEDB home page, select B cell Search or T cell Search.
Under 'Epitope,' click the Organism Finder to enter the source organism of interest. Select from list of common selections (click on the selection and hit Apply Selection).
If your organism is not in the list, type the genus/species under Find (Use NCBI taxonomy) and hit 'Search.' The Finder will locate your entry within the taxonomy tree and it will be highlighted in blue. Click on this and once the organism appears in the Current Selection box at the top, click Apply Selection.
Next, use the Host Organism Finder under the Immunization section to select host.
In the same section, click and expand 1st In Vivo Process. Choose In Vivo Process Type from the list = Administration in vivo.
Next, click and expand the 1st Immunogen section and use Epitope Relation to select Epitope.
If you are looking for epitopes tested in vitro using human samples, leave the 1st In Vivo Process section blank and do not choose Epitope Relation = Epitope. Studies testing correlates of protection in humans seldom include the administration of epitope to the subject. Instead, simply choose host = human and the organism (pathogen) of choice.
Under T cell or B cell Assay section, use the Assay Finder to select neutralization/inhibition assay, cytotoxicity assay, etc. Apply selection.
In this same section, click and expand Antigen to select 'Type' = ' Organism.'
At the bottom of this page, hit 'Search' and this will generate a set of Search Result Summary tables. Note: protection may have only been defined in B cell or only in T cell assays. If you get zero results, try the other assay type.
Find Epitopes at the top of the table and see the value in blue showing the number of epitopes reported for specified assays showing functional activity against the organism of interest.
Click on the value in blue to see detailed information relating to epitope reference, structure, immunization processes and assays.
Results may include multiple pages and can be downloaded through the green Excel-based Export all results link. If desired, return to the IEDB home page to run a second query for T cells, if you chose B cells to begin with.