Help with Common Queries

Below is a list of common queries (CQ) organized by subject. These queries have been designed to parallel the IEDB meta-analysis efforts. Meta-analyses are performed at intervals to query the database for all data relating to subjects of interest (ex. Influenza, Malaria, Tuberculosis). The queries below represent a simplified version of such analysis. Click on the button (+) next to each query for step-by-step instructions on how to find the answer. To get the most out of this tutorial, we suggest that you view this window side by side with the IEDB website. Should you have any questions or feedback, please visit our support forum. Data generated through use of the tutorial can be downloaded for further analysis using Excel. When available, the option to download data appears in the upper left-hand side of the page (Excel icon). Tools for performing specific analyses are also available through the Analysis Resource on the IEDB website. These include B (linear and structural) and T cell (class I and class II) Epitope Prediction, Population Coverage, Homology Mapping, Epitope Conservancy Analysis, as well as Epitope Cluster Analysis, and can be found at the top of the page under 'Tools.'

How to do I determine the origin of the IEDB epitope data (PubMed ID or direct submission) for an organism of interest?

How do I determine the total number of epitopes reported for an organism of interest, including the breakdown of peptidic versus non-peptidic structures, as well as the number of positive and negative?

How do I find out the total number of T cell epitopes reported for an organism of interest? How do I then determine the total number of CD4 versus CD8 epitopes?

In the 'Search' interface on the left side of the IEDB home page, click the Organism Finder under the Epitope Source section to enter the source organism of interest. You can 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.
Back on the home page, go to the Immune Recognition Context section to include T cell Response (using the check box) by deselecting all other response types (default includes all four) and then hit 'Search' at the bottom of the page.
This will generate a set of Search Result Summary tables of T cell epitope data only. The Search Result Summary table automatically includes additional information, including assay, reference, epitope source, immunized host and restricting MHC allele data. Click on the values in blue to display further details of the data.
Results may include multiple pages and can be downloaded through the green Excel-based Export all results link.

SIMPLE SEARCH for CD8/Class I or CD4/Class II epitopes:

In order to further identify as specific subset of T cell epitopes within the broader set returned above, hit 'Revise Query' on the Search Result Summary page which will take you back to the Home page. Then, under the Immune Recognition Context section, select Class I (for CD8/Class I) from the pull-down list under MHC Class and then hit 'Search.'
This will generate a set of Search Result Summary tables that includes all reported CD8/class I epitopes. For all CD4/class II epitopes, simply repeat the above process using Revise Search with the exception of selecting Class II.
The Search Result Summary table automatically includes additional information, including assay, reference, epitope source, immunized host and restricting MHC allele data.
Results may include multiple pages and can be downloaded through the green Excel-based Export all results link.

ADVANCED QUERY for CD8 or CD4 epitopes (note that this will retrieve fewer epitopes for which recognition by CD4/CD8 cells has been explicitly shown):

In order to specifically query for the number of CD8/Class I epitopes from an organism of interest, on the 'Search' pull-down tab along the top on the IEDB home page, go to 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) or type in the genus/species under Find (Use NCBI taxonomy). 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, then click Apply Selection.
Scroll down to the T cell Assay section, click on and expand the Effector Cell. Then, under Effector Cell Type, select T cell CD8+ (cell types are in alphabetical order in the menu). At the bottom of the page, click 'Search.'
This will generate a set of Search Result Summary tables that includes all reported CD8/Class I epitopes.
For all CD4/Class II epitopes, simply repeat the above process using Revise search with the exception of selecting T cell CD4+ under Effector Cell Type.
The Search Result Summary table automatically includes additional information, including assay, reference, epitope source, immunized host and restricting MHC allele data.
Results may include multiple pages and can be downloaded through the green Excel-based Export all results link.

How do I find out the total number of B cell/antibody epitopes reported for an organism of interest? How do I then determine the number of linear versus conformational epitopes?

In the 'Search' interface on the left side of the IEDB home page, click the Organism Finder under the Epitope Source section to enter the source organism of interest. You can 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.
Back on the home page, go to the Immune Recognition Context section to exclude all but the B cell Response (check box) and then hit 'Search' at the bottom of the page. This will generate a set of Search Result Summary tables. This set of tables represents B cell epitope data only.
The Search Result Summary table automatically includes additional information, including assay, reference, epitope source and immunized host. Click on the values in blue to display further details of the data.
Results may include multiple pages and can be downloaded through the green Excel-based Export all results link.

SIMPLE SEARCH for linear or conformational B cell epitopes:

In order to specifically query for just the number of linear antibody epitopes, go back to the IEDB home page by hitting 'Revise Search.' Under Epitope Structure, use the radio button to select 'Linear Peptide' ('Any' is the default). Again, hit 'Search' at the bottom of the page.
This will generate a set of Search Result Summary tables that includes all reported linear B cell/antibody epitopes.
In order to specifically query for the number of discontinuous/conformational antibody epitopes, go back to the IEDB home page by hitting 'Revise Search.' Under Epitope Structure, use the radio button to select 'Discontinuous Peptide.' Again, hit 'Search' at the bottom of the page.
The Search Result Summary table automatically includes additional information, including assay, reference, epitope source and immunized host data.
Results may include multiple pages and can be downloaded through the green Excel-based Export all results link.

How do I generate a list of all the different species and strains reported for an organism of interest?

How do I generate a list of all MHC alleles that have been reported to present epitopes from an organism of interest? Can I select a specific host?

In the 'Search' interface on the left side of the IEDB home page, click the Organism Finder under the Epitope source section 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.
Go to the bottom of the home page and hit 'Search.' This will generate a set of Search Result Summary tables.
Find Restricting MHC Alleles in the Summary table at the bottom and click on the value in blue to display the list of all alleles reported to present organism of interest-specific epitopes.
Click on any desired allele/haplotype in the list (in blue) in order to view the structure, reference and assay information. Details for the assay and immunization process can be accessed by clicking on the assay tab and then clicking on the ID number on the far left-hand side of the resultant table.
This data may include MHC binding data, MHC ligand elution data, functional T cell assays (proliferation, CTL, ELISPOT, etc.) or a combination of all three types of data. The table may also include alleles, haplotypes or simply loci, as reported MHC restriction data is often determined at different levels.
Results may include multiple pages and can be downloaded through the green Excel-based Export all results link.

To select all alleles from a specific host:

Hit 'Revise Search' and select the Host Organism finder under Immune Recognition Context and select your species of interest (ex. Homo sapiens, Mus musculus, etc.) - hit Search.
You can also search for MHC restriction data by specifying a class or alleles of interest.
For this, click on the Allele Finder under MHC Restriction in the same section.
Once the Allele Finder window appears, look under Find. Use the Organism, Class and Allele fields to select the data of interest and hit 'Search.' When the allele/haplotype/loci of interest appears in the list below, click on the blue value.
This value will then appear in the Current Selection box at the top of the screen. Hit Apply Selection. Note, you can select multiple alleles by clicking on additional selections from the list or the entire list by using the Add All On Page button at the top.

How do I generate a list of all proteins from which epitopes have been identified for an organism of interest?

How do I generate data for all host species in which immune responses defining epitopes have been reported for an organism of interest?

In the 'Search' interface on the left side of the IEDB home page, click the Organism Finder under the Epitope Source section 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.
At the bottom of the home page, hit 'Search' and this will generate a set of Search Result Summary tables.
Find Host Organism at the bottom of the page. The value in blue represents all hosts (all species) in which epitopes from the organism of interest were defined.
Click on this value to view the list of all hosts.
To search for data described for a specific host from this list, copy the host organism name from this list and return to the IEDB home page by hitting the back arrow twice, then paste this name in the Host Organism finder under the Immune Recognition Context section. Proceed as above to 'Apply' this selection to your modified query. Hit Search at the bottom of the page.
You now have a list of all epitopes reported for that organism and described in a specific host. If, for example, data were generated from people of a specified geographic region, this will be designated in the list as 'Homo sapiens Vietnamese.'
The Search Result Summary table automatically includes additional information, including assay, reference, epitope source, immunized host and restricting MHC allele data. Click on the values in blue to display further details of the data.
To see the amino acid sequence of epitopes recognized by humans, 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.

How do I search for human data and specify geographic region?

How do I generate data for all epitopes that have been reported for a specific human disease associated with a organism of interest?

On the 'Search' pull-down tab along the top on the IEDB home page, select B cell Search or T cell Search (if both are of interest, perform one at a time).
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 'Homo sapiens.' Apply selection as above.
Under this same section, click to expand 1st In Vivo Process and click on the Disease Finder (grey button) under Disease State.
In the center of the Finder use Find: to search for the disease by typing in its common name or by using ICD10. For example, type 'hepatitis C' for disease related to HCV. Select the disease from the hierarchical list and hit Apply Selection at the top of the window.
If your selection does not appear, please use ICD10 help. Go to http://apps.who.int/classifications/apps/icd/icd10online/].
At the bottom of this page, hit 'Search' and this will generate a set of Search Result Summary tables. Find Epitopes in the top table and see the value in blue showing the number of epitopes reported for that disease of interest.
Click on these values in blue to see detailed information relating to epitope reference, structure, immunization processes and assays.
To see the sequence of epitopes associated with this disease, 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.

Alternative: You can search for associated disease states/syndromes by the infectious disease organism.

For this, perform a search for the organism of interest as above to generate the set of Search Result Summary tables.
Click on the blue value under All in the Assays table and on the results page, click on Excel download [full].
Open the Excel export and scroll over to the 1st In Vivo Disease State column. This column will list any and all disease states reported during the course of epitope definition from the organism of interest.

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?

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 '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).

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?

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.
Alternatively, you can repeat these search criteria in the 2nd In Vivo Process section: choose In Vivo Process Type from the list = Administration in vivo.
In this same section, click and expand 2nd Immunogen to select Epitope Relation = Epitope.
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.

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?

Is it possible to generate a list of epitopes identified as cross-reactive against different strains of the same species? Can I look at reactivity across genera?

How do I add different elements or criteria to my query?

If I want to drill down into the data presented by the Search Result Summary, what is the best approach?

The IEDB provides user further support which can be found on the main menu along the top of the IEDB Home page under 'Support.' Additional tutorials and help can be accessed through the IEDB Zen desk.