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EndNote: 2. Saving, sorting & searching your EndNote library

A guide to using EndNote 20

Updating online references

1. Highlight the reference

2. Right click > Find Reference Updates.

3. EndNote will highlight the differences in a side by side comparison.

4. You can choose to Update Empty Feilds only, Update All Fields or copy & paste select information.

Deleting references from your library

1. Highlight the reference you want to delete.

2. Go to References > Move References to Trash.  edit

Editing references in your library

1. Highlight the reference you want to edit.

2. Select the PDF & Quick Edit tab in the bottom pane in EndNote X5 (Reference tab in EndNote X6 on)Alternatively, double click on the reference to open in the complete window.


Managing Your EndNote Library

Saving your library

It is highly recommended that you make a back-up copy of your EndNote library to guard against damage/loss. This also enables you take your EndNote library with you to another location and to email part or all of your library to your colleagues. Your library in EndNote comprises a .enl file and a .DATA folder which holds various files connected with the library. Both Save a Copy and saving your library as a compressed library includes the .DATA folder.

Use these 2 different methods for different purposes:

1. Save as a Compressed Library to a USB / external drive for moving between computers or sharing: 

  • Open your EndNote library.
  • Go to File > Compressed Library (.enlx)...
  • A dialogue box will appear.


  • Choose to Create the compressed library or Create & Email (launches your default email system with the compressed library file attached) ; With orWithout File Attachments ; including All References in Library or Selected Reference(s) or All References in Group/Group Set.
  • Click Next and save it to your USB.

To restore your compressed library file:

  • Open EndNote.
  • Find the stored file and double click on it.
  • The .enlx file extension (indicating a compressed library) will change to .enl (indicating that it is uncompressed).
  • You can now add references to your library from any computer.  

Note: EndNote X7 & X8 libraries are compatible across platformsyou can create your library on a MAC, save it as a compressed library on a USB then open it on a PC (and vice-versa).   


2. Save a Copy of your library on a USB / external drive as a back-up at a specific point in time.

  • Open your  EndNote library.
  • Go to File > Save a Copy.
  • Include the date in the file name and save it on a different drive / USB as a back-up copy.
  • If you then want to add to & work with this copy you must subsequently save it as a compressed library - each time you Save a Copy a different copy appears (i.e. it doesn't overwrite the existing file).

Searching your library

1. You can quickly search your complete EndNote library for a reference:




  • Click on All References.
  • Type the author surname or keyword in the Quick Search box located in the toolbar & press the Enter key.
  • The drop-down menu provides access to other searches you have conducted.


2. For more options when searching, use the Search panel. To access this search panel in EndNote X6 & X7:

  • Maximise your library window.
  • Click on the Show Search Panel arrow.  




  • The following search box will appear at the top in EndNote X7 and in the bottom panel in EndNote X6:




  • Use the drop-down menu to choose the field you want to search (e.g. author, abstract, keyword etc.)
  • Choose PDF from the field menu to restrict your search to the attached PDF files ; Any Field + PDF to search any field and all PDFs.
  • Use Boolean Operators (AND, OR, NOT) to combine words ; asterisk for truncation e.g. pregnan* finds pregnancy, pregnant.
  • Tick Match Case only if searching for specific capitalisation of the words.
  • Tick Match Words only if searching for specific references containing exactly those words.
  • Use + to add a search line;  - to delete a search line.
  • Click Search. The retrieved references will appear in a temporary Search Results group.


Sorting your library

  • When you open your EndNote library you will see the different parts of each reference displayed under headings such as AuthorYearTitleJournal etc. Clicking on any of these headings enables you to order your references via this part either alphabetically or chronologically.
  • To reverse the order click the arrow head that appears in the heading that currently determines the order.

To make other changes to the EndNote display in the main library window:

  • Go to Edit > Preferences > Display Fields
  • A dialogue box will appear.
  • Use the drop-down menus to change what is displayed in a column then click OK.
  • To revert to the original settings click Revert Panel > OK.


Marking and rating references in your library

You can mark your references as read by clicking on the grey dot which will un-bold the reference (to reverse simply click on the dot again):



To give your references star ratings: Highlight the reference > click on the required number of stars in the Rating column:



 You can search your library for all references of a certain rating:


  • Go to the Search Panel > select Rating from the dropdown menu > choose the rating number of stars > click Search

Find and Compare Duplicates

1. In EndNote click References > Find Duplicates

2. EndNote will present 2 references at a time to compare with any fields that differ highlighted.


3. Scroll to compare > click Keep This Record button above the reference you want.

NOTE: If you have more than one duplicate for a reference you will only be presented with 2 references each time (e.g. initially presented with duplicates 1 and 2 , you discard 2 and you will then be presented with duplicates 1 and 3).

Deleting Multiple Duplicates Simultaneously

1. Click References > Find Duplicates

2. The same window will appear. Instead of choosing which reference to keep click Cancel



3. A temporary Duplicate References folder will appear with all but one of each duplicate reference highlighted.


4. In the EndNote toolbar click References > Move References to Trash. The highlighted references will be discarded.

5.  Records are compared only by primary author, publication year and title - the highlighted references may have extra content (e.g. PDF attached, URL) that you prefer to the citation chosen by EndNote. To change the reference selected for keeping hold down Ctrl key (or Cmmd on a Mac) and toggle the selection.

Automatically Discard Duplicates

1. Go to Edit > Preferences > Duplicates

2. Tick Automatically Discard Duplicates > OK

WARNING: As above, the new duplicate reference may have preferred fields to one already in your library - use this preference with caution

Setting preferences for your library display fields

1. EndNote will allow you to change the name of its set display fields that appear in the library window.


  • Go to Edit > Preferences > Display Fields
  • Change one of the Field columns (e.g. Column 6: Rating) to Label using the drop-down menu.



  • Type the appropriate heading (e.g. Study Design) in the Heading box.
  • Click Apply > OK.




  • Open a reference.
  • Scroll down to the Label field and add the study type e.g. Systematic Review.
  • Save your reference by clicking the second X > Yes.
  • Your reference now displays the label Systematic Review under the column Study Design.  

Changing capitalisation in your library

EndNote will allow you to change the case of a particular field in all the references showing in the library window:

  • Choose the group of references you wish to alter globally (this can be Imported References, All References or any group you have created).
  • Go to Tools >  Change/Move/Copy Fields...
  • A dialog box will open.


  • Select the field you want to change e.g. Title
  • Select Change case & use the drop down menu to choose from Sentence case; lowercase; UPPERCASE; Capitalize Each Word; tOGGLE cASE; Headline Case.  
  • Click OK.                         

Note: the change will apply to all references in the selected group (i.e. that appear in the library window). It is recommended that you make a back-up copy of your library before making such changes.                            

Setting preferences for opening your library

EndNote comes with an Example library you can use to try out features & the option to create several more libraries (although the recommendation is to create only one library & sort your references using Groups). To set EndNote to automatically open displaying the library of your choice:

  • Open the required library in EndNote.
  • Go to Edit > Preferences > Libraries.
  • A dialogue box will appear.


  • Choose Open the specified libraries from the drop-down menu.
  • Click Add Open Libraries > OK.