How do I generate data for all epitopes that have been identified as protective in vivo (epitope used to immunize prior to live challenge) against the organism of interest?
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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 in the Immunization section (using the same technique as provided above for Organism Finder) to select host.
Under the same section, click and expand 1st In Vivo Process section to choose In Vivo Process Type from the list = Administration in vivo.In this same section, click and expand 1st Immunogen to select Epitope Relation = Epitope.
If you are looking for protective epitopes from human subjects, search using in vitro correlates (above query). Studies testing protection in humans seldom include the administration of epitope to the subject, but rather use in vitro correlates.
Scroll down to the B or T cell Assay section, click and expand Assay. Use the Assay Finder to select specified assays or you can multi-select all protection assays [B cell: Protection After Challenge, Protection from Fertility, Survival After Challenge, Weight Loss After Challenge. T cell: Challenge Assay (increased host survival, decreased tumor burden, decreased infectious agent number)].
In this same section, use 'Type' to select Organism from the pull-down list. This will allow for the retrieval of data from the source organism. as well as all related strains.
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 got zero results, try the other assay type.
Find Epitopes in the top table and see the value in blue showing the number of epitopes shown to protect against the organism of interest in vivo.
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.