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EndNote 8: What is an EndNote Library?

A Guide for Toronto Public Health Staff

EndNote x8

EndNote version 8

Planning Ahead: Your EndNote Library & EndNote Online Account

EndNote files are called EndNote Libraries.

Each EndNote Library has two parts: a Data folder and an ENL file.

  • EndNote files have a ENL file extension (i.e. MyLibrary.enl). There should be a Data file with the matching file name.
  • Compressed EndNote libraries have an ENLX file extension (MyLibrary.enlx). These contain both the ENL file and the Data folder.

There are many ways to use EndNote to organize your research evidence.

  • Option 1: Use one EndNote library to save references from all your research projects.
  • Option 2: Create separate EndNote Libraries for each research topic or project.
EndNote Advantages Disadvantages

Option 1:

Use one EndNote (Desktop) library to save references from all your research projects.

You can easily sync to your online EndNote Online Account & access all your data from any computer or tablet which has internet access.

Disadvantage 1: EndNote Online does not track items in "Group Sets" so your records will be scattered (i.e. groups sets are not maintained).

Mitigation Strategy 1: In EndNote Desktop explicitly name Group Sets and Groups according to each project:

  • school nutrition_2018_ERIC
  • school nutrition_2018_CINAHL
  • school nutrition _ 2018_MEDLINE
  • smoking cessation_2019_MEDLINE
  • smoking cessation_2019_CINAHL

When you sync in EndNote Online, the results will be gathered based on the group name.  

Disadvantage 2: One large library can easily get disorganized.

Mitigation Strategy 2: Limit the clutter in EndNote by staying organized:

  • delete items promptly
  • empty Trash  
  • file imported references into Groups right away,
  • use clear and consistent naming conventions for Groups or Group Sets etc.  

Disadvantage 3: Having multiple projects in one EndNote Library requires careful decision making about what you share (i.e. Groups, Group Sets or an entire EndNote Libaray) and with whom.

Mitigation Strategy 3: When working with collaborators on a variety of projects, you may sync your Entire Library to EndNote Online but only  share EndNote Groups with specific collaborators (rather than sharing your entire EndNote Library).

Disadvantage 4: Smart Groups may capture results unexpectedly from other research projects.

Mitigation Strategy 4: Be careful about the search criteria you apply when you create Smart Groups (set specific criteria or add criteria to ensure search function is capturing literature from the appropriate research project).

Option 2:

Create a separate EndNote Library for each research topic or project.

You can organize each research project in a discreet EndNote Library


Projects files are distinguishable.

To collaborate with others, you would copy the appropriate library and email it to them

share Groups or share your compressed EndNote Library (ENLX) file. 

Disadvantage 1: EndNote (x8) only allows you to sync 1 Library to EndNote Online.  

Mitigation Strategy 1: Rather than using EndNOte Online, use these options to share EndNote Libraries with colleagues:

  • create a compressed EndNote Library and send via email
  • save a copy of an EndNote Library and send via email
  • consider exporting references from a specific Group or Groups as a RIS file and send via email (this can be imported into other bibliographic management software)
  • export records in CSV format and email as an Excel file
  • export bibliographies in APA format (with abstracts) and copy into MS Word (if needed, this could be converted into a format for importing into bibliographic management software) 

Do's and Don's


  • Be consistent about where you save your EndNote Libraries.  
  • Keep your DATA folder and ENL file together. The EndNote Library is unusable if you don't have both parts. 
  • Use proper naming conventions if you have multiple EndNote Libraries (descriptive names). If you save an EndNote Library on Network drives, some staff notice that the files are very slow to load (and the vendor indicates that file contents become corrupt over time).  
  • Keep a backup of the EndNote Library (in case you have any issues).
  • DON'T save your only copy of the EndNote Library on a network drive (G or H drive).
  • DON'T save or backup EndNote libraries in cloud storage folders or file syncing apps (DropBox,Google Drive, OneDrive, Sync, etc.)


Did you know?

There is no "save" or "Edit > undo" option in EndNote.  Simply close your EndNote library when you're finished. When you re-open the EndNote program, it will automatically open the last Library you used.