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EndNote: EndNote and Research Projects

Use EndNote to gather and organise references for your assignments and projects

EndNote and large projects

A reference management tool is relevant at various stages of the research/ writing process. The following refers specifically to EndNote20.  Similar guidance will apply if you prefer to use another product, e.g. Mendeley.


Reading/ watching

  • Add the references for your sources into EndNote (or preferred product) as you access them.  [This can be for any of your current, or even future, projects].

Planning an assignment or project


  • Open the EndNote tab on MS Word - see Citing with MS Word.
  • Select the relevant presentation style, e.g. Cite Them Right.
  • Insert your citations as you write.
  • See your automatically generated reference list develop.

Groups or Smart Groups

You will likely be using multiple custom groups to manage the volume of references and different aspects of your projects.

Group Sets make organising these easier but this takes time to organise and maintain.

Smart Groups sometimes remove this time requirement.

With Smart Groups, you set the criteria in advance and EndNote automatically adds any matching references to that group on import.  It is therefore recommended to set your criteria carefully, e.g. year and topic.

Working with your PDFs in EndNote

To annotate a PDF attachment within EndNote 20.

In your EndNote20 library:

  • Click the reference to select it.
  • From the main menu, select 'References' then 'Edit references'.
  • Open the attachment then select the menu and sub-menu items to:
    • Add sticky notes.
    • Highlight or strike through text.
    • Resize the page display.

Remember to save your changes when closing the file.

Checking for duplicate records

If you import references from more than one source, you are likely to have duplicate entries.  EndNote can help you to manage these.

To find duplicate records:

  • Highlight 'All References' or the relevant group.
  • Select 'Library' from the EndNote menu bar.
  • Select 'Find duplicates'.
  • A pop-up window will display with 2 boxes, showing both entries.
  • You can compare these individually and select the best record to keep - an option if you are working with a small number of items.
  • Alternatively, and more appropriately for large numbers of records:
    • Click 'Cancel' on the pop-up box - this highlights all the identified duplicate records.Screenshot EndNote20 highlighting duplicate records
    • Drag all shaded references to EITHER a new custom group - useful if you need to record numbers of duplicates - OR to the 'Trash' (appears in the left panel under 'All References').

A further manual check is also recommended however - EndNote looks for exact matches in the author, title and year fields so won't identify items which differ even slightly.

To display any remaining duplicate items next to each other:

  • Click the 'Title' column header - this sorts the list and displays the references in order by title.
  • Drag duplicate references as above.

Standalone bibliography

Want to generate a standalone bibliography?

  1. Select relevant references in your EndNote library - click on the first entry, hold CTRL then click on the others to make your selection.

  2. Go to File on the EndNote menu bar.

  3. Select Export.

  4. A "Save as" window will appear.  Select your destination folder.

  5. Change the file name.

  6. We recommend selecting Rich Text Format to enable any word processor to open the file.

  7. Select the preferred referencing style.

  8. Ensure 'Export Selected references' is checked.

  9. Confirm.

Merging documents

How do I merge multiple documents, and reference lists, into one?

Complete individual chapters/ documents as normal.  Once you are ready to publish,

For each chapter/ document:

  • Open the EndNote tab in MS Word.
  • Highlight the relevant section, or entire document, as relevant.
  • Select the 'Convert citations and bibliography' option.
  • Select 'Convert to unformatted citations'.
  • Instant Formatting will be automatically turned off, your reference list will be removed and default placeholders will be placed around your citations.

Merge the individual documents into a master document - we recommend creating a new document for the master.

When ready,

  • Select the 'Convert citations and bibliography' dropdown as before.
  • Select 'Convert reference manager citations to EndNote'.

Your citations and reference list should now display correctly and be integrated. 

Manuscript matcher

Once you have completed a large project, you will likely be looking to publish.  EndNote can help with this.

  • Select Manuscript Matcher from the EndNote tab in MS Word
  • Enter your title
  • Add your references
  • The system will look for similar entries elsewhere then display a short list of related journal titles.  

EndNote Training (2018) Manuscript matcher.  Available at: (Accessed: 31 August 2020).

Amending an output style

Occasionally, you will be expected to include elements in your output style that are not pre-set. When this applies, amend the style as necessary.

Firstly, set the default style to display in the 'Style manager'.

  1. Go to 'Edit' in the EndNote menu bar.
  2. Select 'Output Styles' then 'Open style manager'.
  3. Tick the styles you wish to display.
  4. Close.

Secondly, edit the style:

Go To 'Edit' in the menu bar

Select Output Styles, Edit [selected style]

A pop-up window will display.

Screenshot Output Styles Menu

From the panel on the left, select Bibliography, Templates.

Select the relevant template.

Amend as relevant, for example:

Place yout cursor at the relevant point within an item template then select 'Insert Field'.

include any relevant spacing and punctuation.

Close then 'Save As' as relevant.

The new style will appear in the list of styles available from the EndNote tab in Word.

Note: this is a local change and only applies to the device using EndNote X9.

See Editing Reference Types & Styles: Windows for a full list of amendments you can make to reference types and output styles.

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This work in this guide is licensed under a Creative Commons Attribution 4.0 International License.