How do I generate data for all epitopes that have been identified following natural infection or experimental immunization in humans with respect to the organism of interest?

• From the 'Specialized Searches' pull-down menu along the top on the IEDB Home Page, select B cell Assay Details or T cell Assay Details. This will open a new interface with search panes along the left-hand side.
• From the 'Epitope' pane, use the text box next to 'Organism' to type in the organism click the pathogen or other organism of interest (auto-complete feature will help here). Open the Organism Finder only if your choice is not immediately found in the auto-complete list.
• 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 'Homo sapiens'. Apply selection as above.
• Under the same section, click to expand the 1st In Vivo Process section and choose In Vivo Process Type from the list = Occurrence of Infectious Disease (natural infection).
• Then, expand the 1st Immunogen section and use 'Type' to select Organism from the pull-down menu. This will allow for the retrieval of data from the source organism. as well as all related strains.
• Scroll down to the B or T cell Assay Section. Click and expand Antigen to use the Epitope Relation to select Epitope. At the bottom of this page, hit 'Search' and this will generate a set of Search Result Summary tables.
• Find Epitopes at the top of the table and see the value in blue showing the number of positive epitopes reported following natural infection with the organism of interest in humans.
• Click on the value in blue to see detailed information relating to epitope reference, structure, immunization processes and assays.
• To see the sequence of epitopes associated with natural infection, click on T cell or B cell Response in the Assays table.
• 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.

For a list of all epitopes that have been identified following immunization in humans with respect to the organism of interest, perform the same steps as above with the exception of selecting In Vivo Process Type from the list = Administration in vivo (experimental or clinical immunization/vaccination).