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EndNote: Importing Folders of PDFs

Using EndNote--Mayo Clinic's licensed bibliographic database manager

Importing PDF Folders to Create New References

This feature allows you to convert existing collections of PDF files into EndNote records with minimal typing and copying by extracting Digital Object identifiers (DOI) from PDF files. The system matches DOI information with data available from CrossRef ( by capturing bibliographic content and creating new EndNote records.

To import a PDF folder with PDF files:

  1. Open the EndNote library into which you want to import the references.

  2. From the File menu, select Import > Folder to open the Import Folder dialog.

  3. Click the Choose button to open the Browse for Folder dialog.

  4. Select the needed PDF folder, and then click OK.

  5. If the selected folder lists subfolders, click the "Include files in subfolders" check box to include PDF files in those sub-folders in the import operation.

  6. Select the PDF option from the Import Option list.

  7. Select an option from the Duplicates list:

  • Import All: Imports all references, including duplicates.
  • Discard Duplicates: Imports all references except duplicates.

  • Import into Duplicates Library: Duplicate references are imported into a library called File-Dupl.enl, where ”File" is the name of the library into which you are importing.

By default, a reference is considered a duplicate when the Author, Year, Title, and Reference Type match a reference already in the library. See Duplicate Preferences if you would like to change the duplicates criteria.

  1. Click the Import button to import the PDF files from the selected folder to your library.