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EndNote Guide: Basic settings

Use the Edit menu.

These are the most important settings.

  • In EndNote > Edit > Output Styles > Open Style Manager > select NLM
  • In EndNote > Edit > Import Filters >
    Only if the online databases you use are not already on the list, go to the EndNote Download page, search for the database and download its filter.  Filters are used to transfer information previously downloaded from an online database.  
  • In EndNote > Edit > Preferences > Find Full Text:  Checkmark all four full text search options.
    The image below will be updated to show proper settings, as follows:
    • leave OpenURL textbox blank
    • leave URL textbox blank
      Unfortunately the utility our library uses to find full text is incompatible with EndNote.
      The Find Full Text tab explains an alternativre method.
    • uncheck Automatically invoke Find Full Text on newly imported references
      This option is misleading because the EndNote looks for text files instead of PDFs.  it will bog down your system.


  • In Edit > Preferences > Read/Unread:
    Uncheck "Show unread references in bold text". 
    Leave checked if you are different than most people and actually like this feature.



  • Edit > Preferences > PDF Handling.
    If you enable automatic importing, you can place a PDF or other document in a "watched folder".   EndNote will automatically upload the PDF and attempt to create a reference the next time the program is opened.  

Choose a name and path for the "watched folder".  A meaningful filename that begins with "EndNote" is easy to identify.

To automatically rename imported PDFs with a more identifiable name (e.g. Smith2016.pdf instead of a download name of 4321dxtrn6789.pdf), select your preferred renaming pattern. 

See Add References tab for what to expect when importing PDFs. 

During installation, you have the option of establishing credentials for the online account.

  • In Edit > Preferences > Sync :

Enable Sync allows data on installed EndNote to synchronize with EndNote Online. 

Check the Sync Automatically box to have EndNote automatically begin the Sync process every 15 minutes (background processing).  This is recommended.

Do not check the Sync Automatically box if you want to synchronize data manually between installed EndNote and EndNote Online.  You only have to enter your e-mail address and password once in Sync Preferences and not each time you manually synchronize your references between EndNote desktop and EndNote online.

Tip:  Checking box for Sync Automatically is a personal choice. 
"Auto" can flutter while work is in progress.
Unchecking means the user must remember to synchronize.

IMPORTANT:  Run the Backup utility before synchronizing for the first time, and before adding a new device.  

Users who synchronize for the first time, and also users who install EndNote on a new device, must be careful in selecting which account to synchronize.   For example, if a newly established EndNote Online account is empty it can wipe out the Desktop data.  Make a Backup first and review instructions in order to avoid overwriting existing data and PDFs with "data" from the new empty database.

Tip:  Although this is not recommended for new users, if you find the need to have more than one Library, you can change which one syncs with EndNote Online in Sync Preferences at any time. The Sync process begins automatically when you click OK. Again, run BACKUP utility first and be careful which library has the data you want to synchronize.