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EndNote Desktop: X9 & 20: EndNote 101

Created by Health Science Librarians

Quick Tips

Tip #1: After creating an EndNote library, don't delete or separate any folders.

EndNote will generate an EndNote Library file (which is what you click to open your library) and a .Data folder. Both of these must be located together.

In the .Data folder, you'll see one folder named "rdb" and one named "tdb." If you have PDFs in your EndNote library, you'll also see a folder named "PDF." 

These folders contain essential data about each library you create. Never delete them!

For Mac users: EndNote X9 gives you the option to create a "Package" file that contains both the .enl file and the .data folder. This ensures you don't accidentally delete important data. However, if you are using Covidence for a systematic review and using the bulk upload feature, you'll need to access individual PDF files. To do this, save a copy of your library and do not select the Package file option.


Tip #2: Store all of your EndNote libraries locally on your computer; do not store them in the cloud.

If you store EndNote library data in the cloud and then move it onto your local computer, key files in the .Data folder may separate and cause errors in your library. One common error is that PDFs become detached from their citations.

Creating a Library

EndNote Library Basics

  • A library is a collection of references (also called citations). Each reference is stored as an individual record with different data fields for author, title, etc.
  • We recommend that you store all your references in one or two libraries and use Groups and Group Sets (see below) to organize and categorize references.
  • While there is no limit to the number of references that can be stored in one library, we suggest that the number not exceed 100,000.

Creating a Library

  1. Open EndNote. In the dialog box that appears, select Create a new library OR from the menu bar, select File > New.
  2. The New Reference Library dialog box will appear.  Enter a name for your new library.  EndNote will automatically add the .ENL extension, which stands for EndNote Library.
  3. Choose where you would like to save your new library. 
  4. Click the Save button.  The new EndNote library appears.

Opening a Library

  1. Open EndNote. In the dialog box that appears, select Open an existing library OR from the menu bar, select File > Open
  2. A list of libraries that you have previously opened will be displayed.  Select the library that you wish to open.  If the library does not appear in the list, click Open Library...
  3. The Select a Reference Library dialog box will appear.  Locate your library and click the Open button.

Working with PDFs

In EndNote, you can open and annotate a PDF file using the PDF Viewer Panel.

Opening the PDF Viewer Panel

  1. Double click on a reference with an attached PDF file (indicated by the presence of a paperclip symbol).  This will open the reference window. 
  2. Click on the PDF tab above the toolbar.  The PDF Viewer Panel will open.

Using the PDF Viewer Panel

The toolbar at the top of the PDF Viewer Panel has several options that allow you to add notes, highlight text and find words and phrases within the PDF document.  You can hover your cursor over an icon to view text explaining its function.

Add Notes

  1. Use your cursor to highlight the text in the PDF document where you wish to add a note.
  2. Click on the Sticky Note icon in the toolbar at the top of the PDF Viewer Panel.  A Sticky Note icon will appear next to the highlighted text.
  3. Double-click on the Sticky Note icon to display a text box.  Type your notes in the text box.
  4. Click the Save PDF button in the toolbar to save your changes.
  5. To delete a note, click on the Sticky Note that you wish to remove and press the Delete key on your keyboard.

Highlight Text

  1. Use your cursor to highlight the text in the PDF document that you wish to highlight.
  2. Click on the Highlight Text button  in the toolbar at the top of the PDF Viewer Panel.  The selected text will be highlighted in yellow.
  3. Click the Save PDF button in the toolbar to save your changes.

Using the Find Feature

  1. Enter words or phrases in the search box in the toolbar at the top of the PDF Viewer Panel. The Find feature searches within the PDF document that is currently open.
  2. Click on the Next and Previous buttons to navigate to the next or previous instance of your search word or phrase.

Creating Groups and Group Sets

Groups, Group Sets, and Smart Groups

The panel in the left column of the library window displays all the Groups and Group Sets in your library. The Groups called All References, Unfiled, and Trash are built into your library and cannot be changed. Additionally, if you use the Find Full Text feature, EndNote will automatically create a Group Set with 3 Groups titled Found PDF, Found URL, and Not Found. Any time you use Find Full Text for a citation, EndNote will automatically add the citation to one of those 3 Groups. 

Note that when you add a citation to a Group, EndNote makes a copy of that citation that is linked with the "root" citation in your library. Removing a citation from a Group will not delete the citation from your library.


Groups are subsets, or folders, used to categorize and organize references.  Groups can be organized into Group Sets. 

To create a Group or Group Set, select Groups from the menu bar.  Select Create Group or Create Group Set




Group Sets



Smart Groups

When you create a Smart Group, EndNote will automatically add citations into the group if they fit the parameters you have specified. 

Viewing and Organizing References

Viewing References

  1. To view a reference, double-click on its line in your library.
  2. The Reference window will open. 
  3. Here, you can view, edit or enter information for the reference.
  4. To save changes to the reference, select File > Save from the menu, or Ctrl + S on your keyboard.

Adding References to a Group

  1. In the library window, select the references that you wish to move. 
  2. You can then drag the references to the Group, or right-click Add References To from the list of options that appear.  Select the Group to which you wish to add your references.
  3. The number of references in the selected Group will update, indicating that the new references have been added.

Removing References from a Group

  1. In the library window, select the references that you wish to remove.
  2. Remove the references by right-clicking and selecting Remove References From Group, or selecting Groups > Remove References From Group from the menu bar.
  3. The references will be removed from the Group.  They will not be deleted from your library.

Deleting References from a Library

  1. In the library window, select the references that you wish to delete.
  2. You can then delete the references by right-clicking and selecting Move References to Trash, or by selecting References > Move References to Trash from the menu bar.
  3. The Trash Group contains references that you have deleted from your library.  To permanently delete the references  from your library, you can select References > Empty Trash from the menu bar, or  click on the Trash Group in the Groups panel, then right click on your mouse and select Empty Trash
  4. If you do not actively Empty Trash, you will be prompted to do so when you close the EndNote library.

File Attachments

File Attachment Basics

You can attach up to 45 files from your computer (PDF, Word document, Excel document, graphic) to an EndNote reference.

Attach a File

  1. Click on a reference in the library window to highlight it.
  2. Select References > File Attachments > Attach File... (alternatively, you can right click on the reference and select File Attachments > Attach File...)
  3. In the dialog box that opens, select file that you wish to attach.
  4. Choose how you would like EndNote to attach the file by either checking or unchecking the box next to "Copy this file to the default attachments folder and create a relative link"
    • Box checked: EndNote makes copy of original file and places it in the EndNote library folder, so the file is part of the library.
    • Box unchecked: EndNote will look in the original folder for the attached file.  This is helpful if you plan to edit the file and want those changes reflected when you access the file.  However, the file will not be accessible if you move it to another folder or share your library.
  5. Click Open.
  6. The file is now attached to your reference.  For more information on reading and annotating PDFs in EndNote, see Working with PDFs.

Journal Terms List

What are term lists?

Three types of term lists are available with every library file: Authors, Journals, and Keywords.  These lists are linked to their corresponding fields and serve as an index, improving the consistency and accuracy of your references, citations, and bibliographies.

How can I abbreviate journal names?

Sometimes different citation styles use abbreviations for the journal names. EndNote uses the journal terms list to abbreviate journal names. We recommend that you define the Journal term list for each new library. This helps ensure that all journal names and abbreviations are consistent.

Define the Journal Term list

Note: If you did not define your Journals term list when you created your library, then your term list has been created automatically as you enter new references into your library (whether by importing or manually entering them). To ensure consistency and accuracy, we recommend that you discard your existing Journal term list and import Journal term lists from EndNote.

  1. In your library, select Tools > Open Terms Lists > Journal Terms List.
  2. Click on the first journal name and then press [ctrl] + A on the keyboard to select all of the journals.
  3. When all of the journals are highlighted, select Delete Term.

To import a new journal terms list:

  1. In your library, select Tools > Define Terms Lists... from the menu bar.  The Term Lists dialog box will open.

  1. In the Lists tab, highlight Journals, then click the Import List... button.  A dialog box will open displaying the available term lists in your EndNote Program Files. 

  1. Select the term list you wish to import.  For the health sciences, we recommend that you import the Medical and Humanities term lists.  Click Open.  An Updating Term Lists box will appear and, once the update is complete, a different box will display the number of terms inserted into the Journals term list. Repeat for each term list that you wish to add. Click Close when you have finished.

Modify the Citation Style to Use Journal Abbreviations

  1. Select the output style you want to modify by using Edit > Output Styles > Edit [Name of style of want to edit]. If the style you want is not shown, click on Open Style Manager and select it from there.
  2. Select Journal Names on the left column. Under Journal Name Format, select the field you want. This is usually Abbreviation 1.
  3. Save the output style with a new one, such as "APA 6th Edit".

For more information and screenshots on modifying citation styles, see the Advanced Tips.

Create Bibliography

Sometimes you may want to create a document that contains just a bibliography, with no citations. Here is one way to do it.

Creating a Bibliography without Citations

  1. Select the Output Style in which you wish your bibliography to appear from the Styles menu in the toolbar.  The Output Style that you select determines how your references are sorted and formatted in the bibliography. 
  2. Select the references that you wish to include in your bibliography. 
  3. Select Edit > Copy Formatted from the menu bar OR right-click on the selected references and choose Copy Formatted from the menu that appears.
  4. Open a Microsoft Word document.  Place your cursor where you want your bibliography to appear. 
  5. Click on the Paste button in the Word toolbar or select Ctrl + V on your keyboard.  Your bibliography will appear in the Word document.

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