Introducing the IEDB Customized Data Exports

We are thrilled to announce that the long-requested IEDB customized exports are now available to our users! This powerful functionality allows users to customize data exports to better fit their unique requirements by selecting specific fields of interest and various file formats. This article will guide you through the process of using this feature, ensuring you get the most out of it.

We welcome your feedback and comments via email to help@iedb.org.

Step-by-Step Guide to Custom Data Exports:

1. Run your query at iedb.org as you normally would, navigating to the results page. 

2. Select your results tab of choice (Epitopes, Antigens, Assays, Receptors, References) to be exported.  Locate and click on the ‘Export Results’ button in the top right corner.

3. Next, you will see an ‘Export to File’ pop-up, which provides the interface for export customization. User will be able to choose from the following:

• File Format - There are 4 formats available; .XLSX, .CSV, .TSV, .JSON
• Header Row Format - Users can select whether their export should have double headers (the field section and field name) or single header (concatenation of the double headers into a single line) or no headers (mostly used for programmatic analysis and machine learning). Note that the field section header allows users to distinguish between multiple fields that have the same name. For example, Epitope, Immunogen, and Antigen sections all have a field named “Source Organism”, which means Epitope Source Organism, Immunogen Source Organism, and Antigen Source Organism, accordingly.
• Export Type - There are five export types that are already available in the IEDB for those who would not like to further customize the fields for export. These types are:
  • Full, all data columns - this provides a complete export of all the data columns available pertinent to your query. 
  • Default - this provides an export with the most commonly used fields in the database as agreed with research experts and IEDB team members. This export is useful if you are interested in only the most important information in a digestible format. 
  • Default, including IRI columns - this provides you with the most commonly used fields in the database (as above) along with the unique ontology/external resource identifiers (IRIs). These identifiers map terms used in the IEDB to standardized resources such as NCBI Taxonomy, UniProt, The Ontology for Biomedical Investigations, etc.
  • IEDB Website Displayed - this export contains all fields and data points exactly as displayed on the IEDB results page.
  • Custom Export - this option allows you to manually select each field you want to include in your export. If this option is selected, users should look at and expand each option under the ‘Columns to Include’ text, providing greater customizability for researchers.

4. Columns to Include:  The new ‘Columns to Include’ feature should only be used with the ‘Custom Export’ export type. It gives users maximum flexibility with the data they would like to export. You can either select all columns or choose specific ones by checking the corresponding boxes.The below screenshot shows some fields that have been selected (green box) and other fields that have been deselected (white box). 

5. Once you are satisfied with your custom data export settings, click 'Export' to begin the process. Depending on the size of your data set and the complexity of your customizations, the export file may take a few seconds to a minute. It will be automatically downloaded to your computer when complete. 

It is important to note that the customization options will reflect the results tab that you are on (i.e., Epitopes, Antigens, Assays, Receptors, References). This means that if you are looking at the ‘Epitopes’ tab and select ‘Export Results’, you will be presented with all the field names available in that particular tab. If you are interested in obtaining antigen data, for example, you must select the ‘Antigen’ results tab and hit ‘Export Results’. At this stage, there is no single step to export all results from all tabs at once. 

Export Scenarios for Consideration:

There are some scenarios to consider with the implementation of the customized data exports, and we detail these below. 

• Exports with over one million rows of data - in the case where you are exporting over one million rows of data, the information will be split across two tabs in Excel. Please note that if you have selected the header option, the headers will display on the first tab but not on the second. Overall, due to size limitations, approximately every million rows of data will lead to a split onto a new tab.

Additional New Features:

1. Help Tab - We now provide a second tab of the export that gives a brief explanation of what each exported field name means, termed “Description of Field.” We also provide 3 rows of example data, broken down into two rows of actual data as it exists in the IEDB website called “Example“ and one row called “Other possible values,” which shows an example value for every field, but these values do not necessarily go together. We also provide “Help Topic Link” which is a link to the help desk article for that field, when one exists.

Query Parameters - We now provide a third tab of the export that contains the parameters that were used to generate the query being exported, as well as the date of database build when that data was queried and exported. This enables users to know which version of the IEDB was queried (as we update the database weekly) in the event you need to re-query the IEDB and obtain updated results, or contact the IEDB team for assistance.