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EndNote desktop guide: Tips and Tricks (EndNote X9)



BU Harvard

Screening references quickly

Storing your library

Synchronising your desktop library with your EndNote online account

Sharing your library

Writing for publication


Creating a stand alone bibliography

If you do not want to use Cite While you Write to build citations and references in your Word document and you just want to create a stand alone bibliography, you can do this quite simply.

From within your library:

  • Select the referencing style you require from the menu at the top of your library
  • Select the references you want to include in your bibliography (it might be easiest to compile them together as a group first)
  • Select Edit > Copy Formatted

In your Word document:

  • Right click where you want to insert the bibliography
  • Select the icons for either Keep Source Formatting or Merge Formatting
BU Harvard

Adding the style to EndNote

To add the BU Harvard style to your computer, please see the section on adding extra output styles

Specific instructions related to using BU Harvard

To ensure the BU Harvard referencing style is outputted correctly, remember to change the reference type for the following

  • Journal article > Change to: Electronic journal article
  • Book > Change to: Electronic book
  • Report > Change to: Electronic report
Screening references quickly

Title and abstract screening

One of the major advantages to using EndNote desktop is the ability to quickly review articles at title and abstract level. If you create yourself relevant groups on the left of the screen, you can review the title (centre of page) and abstract (right of page)  and drag and drop refences to relevant groups e.g. include; exclude; unsure)

It also helps to have your monitor in portrait profile (see below)


Screenshot portrait view

Storing your library

Where do I store my EndNote library?

Clarivate advise saving the library to your C:\ drive, but not a networked drive, flash drive or cloud storage. However the University has reviewed the options and suggest you keep it on your H:\ drive (networked drive) when at work. You should NOT keep it on cloud storage or a flash drive. At home, you should keep a copy on your C:\ drive. You must also keep a compressed back up (.enlx file) on your H:\ drive (or other suitable storage, e.g. Cloud, Flash etc.). You can also back it up by synchronising to EndNote online (see our instructions on Sync'ing). This is always necessary and particularly so when using a C:\ drive as opposed to the University network (H) drive as the C:\ drive is NOT backed up.

Related Clarivate guidance.

Synchronising your desktop library with your EndNote online account

Synchronising your desktop library with your EndNote online account

You may synchronise one EndNote library to an online account. If you have a second library that you want to synchronise, you will need to create a second online account. To create an EndNote online account, see our guidance

To synchronse your library, in EndNote desktop

  • Go to, Edit > Preferences > Sync
  • In EndNote Account Credentials, enter the email address and password you use to access your EndNote online account
  • Choose whether you want the desktop and online library to sync automatically
  • Click Apply and then OK

To initiate the sync

  • Click on the Sync Library icon on the top toolbar

Screenshot of sync library

  • A progress status indicator will appear in the bottom right corner of EndNote
  • A sync status report appears in the panel to the left


Remember that the synchronisation process is two way. This means, for example, that if you deleted the references in your online account and then synchronised, all the references would be then deleted in your desktop library. Always remember to keep a backup. If in doubt, please contact us.
Sharing your library

With yourself

So you may want to work at home using EndNote desktop via AppsAnywhere, but your EndNote library is at work on your hard drive. What do you do? The answer is quite simple

  1. At work, synchronise your desktop library with your EndNote online account
  2. On the machine that you want to use, that is not your university machine at work, create a new blank EndNote library
  3. In EndNote, enter your EndNote online credentials:  Edit > Preferences > Sync [enter credentials]
  4. Sync this blank library with your EndNote online library

You now have a replica of the library that is on the C:\ drive of your machine at work. You can work on this library and save changes back to EndNote online. When you get to work, sync your work library with EndNote online and the changes will be pulled back through.

Graphic of EndNote syncing between work C:\ drive, online and other C:\ drive

With someone else

[Caveat: there are two ways to share a library, using EndNote online (which shares individually specified groups) and using EndNote desktop (which shares your entire library to another desktop machine, including attached documents). In this article we are talking about sharing using EndNote desktop]

To share a desktop library with someone else, they will need to have an EndNote online account (for authorisation purposes).

To share:

  1. Synchronise your desktop library with your EndNote online account [you will not be able to use your EndNote online account for any other purpose while it is synchronised with your desktop library]
  2. Click on the Share Library icon    Screen short of share library button in EndNote
  3. Enter the email address of the person you want to share the library with
  4. Click 'Invite'

To receive:

  1. You will receive an email indicating someone has shared a library with you
  2. Following the instructions for accepting that invitation
  3. In EndNote desktop, go to File> Open shared library
  4. The library will download

Changes you make to the library as a recipient will be saved back to the online account of the library owner when you press the Sync Library button. Similarly, changes made by the owner will be saved to the online account of the library owner when then press the Sync Library button and then back to your library whe  you press the Sync Library button.    Sync button screen shot


Due to licensing arrangement which enable access to full text, if you have a library with full text references it is advisable not to share it with colleagues outside of the University.
Writing for publication

Term lists - essential

When you import references of journal articles from databases, they arrive with either the abbreviated OR full journal name as part of the reference, depending on how that database stores references.

This poses a potential problem in that, if you imported a reference that contained the full journal name, but want to write for a journal that requires an abbreviated name in the referencing style, EndNote can only insert the data it has (in this case a full journal name) which would be incorrect. You could amend your reference in your library, but this would be time consuming (for all references requiring this) and you would have to reverse the change if you then wanted to publish in a journal requiring the full journal name .

The solution...?

EndNote desktop (NOT EndNote online) can inset the correct journal format for you automatically, but only if you configure Term Lists for your library (a look up table which is easy to create).

How does it do this? - Example

The 'Journal of rural health' requires an abbreviation of the journal name in it's reference lists, e.g.

Thyer J, Wong J, Thomson A, Bell B, Hyland C, Challis D. Fifty years of RhD immunoglobulin (anti-D) therapy in Australia: celebrating a public health success story. Med J Aust. Oct 15 2018;209(8):336-339.


as defined by the Output style in EndNote

Journal of Rural Health Output Style


but the reference you imported contains the full journal name

Screenshot of record in EndNote library with full journal name


It uses a lookup table

Term Lists table screen shot


to identify the correct arrangement for the output style (in this case Abbreviation 2).

Setting up your term lists

Journal term lists need to be applied to each local library you create. Open an EndNote library, then navigate/click as follows…

  1. Tools
  2. Define term lists [a dialog box will now appear. In the box, navigate/click as follows…]
  3. Lists (tab)
  4. Highlight ‘journals’ (central pane)
  5. Import list [a dialogue box will now appear. Browse the .txt files for an the appropriate term list]
  6. Double click on a file (it should automatically import into your library)
  7. Click OK
  8. Finished!

You can import more than one term list file if your research is cross discipline (repeat the step above).

Editing your term lists

It is best to import a term list when you first create a library, but none the less, your term lists will need to be edited as you build your library. This may be because you imported references before importing your term list (EndNote automatically tries to build term lists) or the journal name in the reference you imported is not matched by an existing record in your term list (EndNote just adds what you have imported).

To edit a record:

Select Edit term to open a dialogue box where the record can be edited

Screen shot of editing term list


Similarly, to remove incomplete but duplicate records, use the Delete Term option

Screenshot delete term list


If you have any questions about term list, please email contact us


Extra output styles (including Harvard(BourneU))

One of the most useful features of EndNote is it's ability to replicate the citation/referencing style of 6000+ journals. Many of the styles are already available to you in EndNote, but more can be found on the Clarivate support pages. To install another style, you need to add it to one of two locations.

1) EndNote program files

The program files contain a folder called 'Styles.' If you add a new style file to this folder, it will then appear in the drop down list of styles available to you. The problems with doing it this way are a) that you will need to ask BU IT Services to install the file as you are unlikely to have administration rights to your machine; b) when a new version of EndNote is installed, additional styles will be overwritten and you will need to install them again.

2) Local folder

EndNote is designed to link to a local folder for additional styles (which avoids the problems of admin rights and program updates). To set this up:

  1. Create a folder for additional styles somewhere in your file structure e.g. somewhere in your H:\ drive, and call it something sensible like EndNote styles
  2. Go to the folder in your computer and add the new style file
  3. In EndNote, go to: Edit > Preferences > Folder Locations
  4. In Style Folder, browse for the folder you created and click Apply > OK. It will then appear in the drop down list of output styles available to you

The BU Harvard style file, Harvard(BourneU) is available just below this box

Important: before you save, change the underscores in the filename back to brackets.

Last update: 13th December 2016.

Output styles (editing)

Output styles are customisable and there are times you may want to make adjustments to a style. For information on how to do this, please contact us.