Skip to main content

EndNote: Synchronising your desktop and online libraries

This software package for managing references (citations) is available free to Monash University students and staff. This guide has information about working with EndNote in the Monash University environment.

Backing up your library

Backing up your library (highly recommended)

Before the first synchronisation, EndNote will prompt you to make a back-up of your library as a compressed file. This will be a single file containing all references and attachments. Click yes to make a back-up, and change the file name and stored location if you wish. If you have a large library the back up may take some time to complete.

When the back-up finishes, EndNote will automatically begin the synchronise process. The time taken to perform the synchronisation will depend on the size of your library and speed of your internet connection.

Synchronise your Desktop and Online libraries

Using the 'Sync Library' feature of EndNote Online allows you to access your library across any platform. It works with EndNote X6 and later versions, but to synchronise the groups in your library, EndNote X7.1  or above needs to be installed.

Synchronising enables you to have two identical libraries (including attachments) - one on the desktop and one online. Synchronising is initiated from EndNote on your desktop. It is not possible to synchronise if you are only in EndNote Online- your desktop version needs to be open. Set your preferences to enable EndNote to automatically synchronise every 15 minutes (background processing), or manually if you prefer.

Syncronising for the first time

To activate the synchronisation process you must first register for an EndNote Online account.

From the menu bar in EndNote desktop select Tools and then Sync.  Alternatively click the icon for Windows  Windows sync icon  or Mac   Mac sync icon .

If you are not already logged into EndNote Online you will be prompted to do so.  If you do not already have an account select the 'Sign Up' option and complete the registration process.

Sign-up option

Note: If you have previously had an EndNote online library check to make sure any references in the library are not duplicates to your desktop library. If they are, you should delete them (and empty your trash file) before syncing, otherwise they will  be duplicated in your desktop library.

After the first syncronisation

Any change made to any synchronised library will be reflected in all synchronised copies of the library. For example, if you delete references from your desktop library they will also be deleted from your online library.

Sync Conflicts

Be aware that a Sync Conflict group may appear in the Groups panel when syncing between your desktop and online libraries

Sync conflicts

This occurs when you edit a reference in both the desktop and online library between syncs.  As a result EndNote does not know which reference you want to keep.

Select the Sync Conflicts group and a dialog box will appear to allow you to resolve the conflict by choosing the reference you wish to keep.

Synchronise your groups and group sets for X7.1 and above

Your EndNote Online library will display all of the references from your desktop library and any custom groups. However if there are group sets in your desktop library this structure will not appear online, and the constituent groups will be organised in alphabetical order.

If you want the groups to be organised in group sets, as they were on the desktop, use the following work around.

  1. Go back into your desktop library
  2. Attach a prefix to the name of each custom group to refect the group set that they are organised under.
  3. Activate the synchronise process again to update your online library . The groups will now be listed in alphabetical order based on their group sets.

Even though the group sets, smart groups, and combined groups do not show in the online library, the information to create them is stored there for transfer to all synchronised desktop libraries.

     Groups display on desktop          groups display online

Changing your synchronise preferences

From the menu bar select Edit, Preferences and then tick or untick the Sync automatically option

Endnote preferences