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Reference management: EndNote


EndNote is a programme that helps you with collecting, organising, citing and sharing references to -and often including the full text of- sources (articles, books, data etc.). Because of the speed and advanced options EndNote is particularly suitable for processing large numbers of publications in systematic reviews.

EndNote is licenced by Utrecht University and can be installed on Windows and Mac, but is not available for Linux. 

Source: Clarivate EndNote LibGuide,

EndNote Support:

EndNote is a Utrecht University licenced programme and so freely available for UU staff and students.

  • UU-staff:
    Follow the explanation on UU intranet (under Reference Management).
  • UMCU-staff
    Via the UMCU IT helpdesk you can request permission to use EndNote. See UMCU intranet.
  • UU-students:
    EndNote is only available via MyWorkplace.

 When you install EndNote, it is also added to your word processing programme.

Get going:

  1. Under Edit>Preferences you can change settings, In any case fill in at "Find Full Text" the following data to improve adding the full text of publications:
    1. OpenURLPath:
    2. Authenticate With:
  2. Create a "library" in Endnote via File>New. Don't save your library in Dropbox, Google Drive or other Cloud Services but on your computer or network drive.
  3. Think carefully about a good back-up (see synchronising and exporting).

Tips & tricks

  • If you are having problems installing Endnote, please contact  UU ITS helpdesk.
  • If the Cite While You Write tool does not appear in  Word, first have a look at Clarivate EndNote Support for Cite While You Write.
  • You can create several libraries in EndNote for each of your projects, but only one library can be synchronised with your online EndNote account.


There are three ways to add literature to EndNote:

Option 1: from the source itself

If you find an article online, you can directly save the title data and (often) the full text in EndNote by EndNote Click. If this extension recognises an article on the website the button below will show. By clicking on that button, you will be directed to the EndNote Click Locker where you will find the option Push to EndNote account.

EndNote Click is available for Chrome, Edge and Firefox. Follow the steps in the installation guide..


Option 2: importing from a  database or search engine

You can export search results from a search engine (PubMed, Scopus etc.) and next import them in EndNote. For instance, if you are collecting literature on a topic in a systematic way.

  1. Export your search results. The options are different for each search engine, for instance they can be found under export, send to or citation manager. Save the file as .ris- or bibtex-file.
  2. Import the file above in EndNote via File > Import.
    Please note that you choose the right import option (many search engines have a separate import filter) and indicate what you want to do with the duplicates.

Check tips&tricks for further information about the major search engines.

Option 3: manually

If other options are not available, you can also add sources manually.
Go in EndNote to Reference > New Reference or click on the button 

Tips & tricks

  • Below you will find the settings you need to choose for the major search engines: 
Search engine Export function file type import filter EndNote Remark
PubMed Send to > Citation Manager .nbib PubMed (NLM)  
Scopus Export RIS format Scopus In any case select Abstracts in addition to citation information!
Web of Science Export > Export to Endnote Desktop .ciw - Open the .ciw file and the references will be automatically imported in EndNote.


Organising your library

  • In the left menu you find groups: these are groups/folders within a library, and may be arranged in sub groups. References can be included in several groups. You can also create Smart Groups to which all references are added that must meet certain criterions (all references after the year 20xx, all references containing keyword X etc.).

Add your own information to references

Double-click on a reference for editing:

  • keywords: often this field already contains keywords that have been included when importing titles. You can change or delete them.
  • research notes: in this field you can add your own remarks to a refererence. The field Notes is less suitable for this use, it often contains information which has been included when adding references to your library.

Automatically supplementing information and adding full text.

  • Not all references you are adding are complete or up-to-date. There is a simple way to improve your literature references. Select all titles you want to update and go to References > Find Reference Updates.
  • You can have EndNote search for the full text of publications and add them to your library. Go to References > Find Full Text.

 EndNote offers several options to deduplicate titles. It is important to select the right settings.


Under Edit > Preferences > Duplicates you can tell EndNote on the basis of which data titles must be deduplicated .You can deduplicate multiple times by different settings.

  • Always choose "Ignore spacing and punctuation"
  • Author, Year, Title, Secondary Title (Journal)
    Reliable option allowing you to deduplicate without having to check. Works best in combination with a list of journals (tips & tricks).
  • Author, Year, Title, Pages
    Reliable option allowing you to deduplicate without having to check. But does not work in the case of differences in page notations.
  • Author, Year, Title
    By this option most duplicates are found, but it also brings the risk of having publications wrongfully indicated as duplicates. That is why it is recommended to apply this option last and in a controlled way.

Deduplicating, controlled

Go to References > Find Duplicates to find duplicates in EndNote. One by one EndNote shows the sets with duplicates and lets you choose which ones you want to keep. 


Deduplicating, automatically

Go to References > Find Duplicates to find duplicates. EndNote shows the first double set of titles.

  • Now select cancel.
  • In the folder with duplicates you now see that all second (or further) versions of a publication have been selected.
  • Click on delete to remove the selected references.


Deduplicating, when importing 

When importing a set of publications from a database, you can already indicate whether you want to import duplicates. You can select from:

  • import all
  • discard duplicates
  • import into duplicates library

This is also a form of automatic uncontrolled deduplicating.

Ontdubbelen in Endote (versie X7, maar vergelijkbaar met versie X9)





Cite While You Write for Word

EndNote offers Cite While You Write (CWYW) for Word. With the help of this add-in you simply add literature references to your text and a reading list of your used sources is automatically generated.
When installing EndNote this option is automatically included in Word (see Installing EndNote).

See these videos for more information.

Creating a bibliography

Also without Cite While You Write you can create a bibliography.

  • Select the publications you want to include in your bibliography
  • Go to File > Export
  • As file type choose rich text format (*rtf) and select the output style of your choice (APA, Chicago, Vancouver, MLA and many others)


Tips & tricks

You can share your EndNote library with a maximum of 100 persons and give them rights to only view them or even to edit them.

  • You can only share the EndNote Library which you are synchronising with your online acoount. If you work with several libraries, you can only share one library.
  • You can also share a part of your EndNote library by creating a group and share it. Right-click on the group and select Share Group. For more information watch this video.

It is also possible to send someone a copy of your EndNote library as it is saved on your computer. But this only works if you send all folders/files belonging to your library. See synchronising and making back ups for further explanation.



You can synchronise your EndNote Library with an online account. The benefits:

  • You will automatically have a back-up of your EndNote Library.
  • You can also give others access to your EndNote Library (Collaborating and sharing).
  • You can also view your references from another computer.


If synchronising is not secure enough, if you want to archive or share a copy of your library or if you want to switch to another reference tool, you have a number of options.

  • Export your references via file>export. Select file type: txt and for output style Refman (ris) export.
    You only export title descriptions with links, keywords etc. The attachments (for instance the PDFs) and your groups structure will be lost. This file can be accessed with any other reference tool.
  • Export your library as compressed library via file>compressed library.
    You export your complete EndNote library, including attachments and groups structure.
    This file can only be opened with EndNote (version X and later).
    You can also use a compressed file as a back up.
  • See also Clarivate page Moving, backing up, or transferring libraries to another computer.