EndNote Desktop

This tutorial will walk you through using the latest desktop version of EndNote.

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Merge Libraries

There are multiple ways to merge library files. The recommended method to use is to Import one library into another. This allows you to filter out duplicates.

Note: Before merging libraries, it is a good idea to make a backup copy of the library into which you are transferring references.

Importing EndNote Libraries:

To import an EndNote library into an EndNote library:
1.    (Optional) If you want to import only a subset of references from a library, first open that library and show only the references you wish to copy. For example, if the library says, “Showing 10 out of 200 references,” EndNote imports only 10 references. If the library you are importing is locked or in “Read-Only” mode, all references are imported regardless of what is currently showing.
2.    Open the library into which you want to import the references.
3.    From the File menu, choose Import.
4.    Click the Choose File button to locate and open the library (.enl file) you want to import.
5.    From the Import Options list, select EndNote Library.
6.    Select an option from the Duplicates list:
 Import All:   Imports the references, including duplicates.
 Discard Duplicates:  Imports the 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.
7.    Choose a Text Translation option.
This option allows you to specify the text character encoding of the file you import, so that extended characters transfer correctly. You can use No Translation for text files that do not contain any extended characters.
8.    Click Import to import the library.
Note: The time required to import an EndNote library is proportionate to the size of the library. Refer to the progress indicator to determine when EndNote has completed the task.

When the import is complete, only newly imported references display in the Library window. This is a perfect time to add a keyword to each imported reference with the Change Field command, or to peruse the imported data to make sure it imported as expected. Make sure to check references that contain extended characters. To return all of your references to the library display (including the newly imported ones), choose Show All References from the References menu.

Using "Copy References to" option in EndNote:

From EndNote X2 and later, the user can use this option to transfer/copy references between two different EndNote desktop libraries.
1. Open the EndNote library from which you want to transfer the references.
2. Select the references that you want to transfer.
3. Do a right click and select “Copy References To”.
4. Here you can either select “New Library” to create a new library with the selected references or “Choose Library” to manually select a library for copying the references.
5. You can also find the recent library in this menu which you can select for transferring the references.


- More options for merging libraries (from EndNote Knowledge Base)

Export to Excel

Method to prepare EndNote Library copy for export to Excel:
Remember to back up your library first, then save a copy to prepare for export as tab-delimited style for Excel.  Prepping the temporary copy of EndNote library for a tab-delimited export requires removing the carriage returns in all fields, then adding carriage returns back to the author fields before export. Detailed Instructions at EndNote Support article on exporting references to Excel.

Basic Steps: (after backing up your library > File > Compressed Library (.enlx))

Save a copy of library > File > Save a copy
Open the copy and prepare the copy for export: to Excel:

  1. Go to Edit > Find and Replace
    1. Set Select a Field to Any Field
      1. Place cursor in the Find box
        1. Click Insert Special button
        2. Insert a Carriage return
      2. Place cursor in the Replace box,
        1.  Type two slashes (//)
      3. Click Change
  2. Go to Edit > Find and Replace
    1. Set Select a Field to Author
      1. Place cursor in the Find box
        1.  Type two slashes (//)
      2. Uncheck "Match Words"
      3. Place cursor in the Replace box,
        1. Click Insert Special button
        2. Insert a Carriage return
      4. Click Change
  3. Repeat step 2 for
    1. Secondary Author
    2. Subsidiary Author
    3. Tertiary Author
    4. Translated Author

Export prepped copy of EndNote Library (.txt)  to Excel:

  1. In EndNote go to Edit > Output Styles > Open Style Manager
  2. Place a check next to "Tab_Delimited_RefNumber" and close the Style Manager window
  3. Go to File > Export and save the file as a "Text File (*.txt)" making certain to set the output style to “Tab Delimited".
  4. Save this file.

This saved .txt file is what you will then open using Excel. Refer to the Excel documentation for how to open the tab delimited file.