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EndNote Desktop: Collecting References

Help with using EndNote Desktop

Creating an EndNote library

  • Open EndNote EndNote program from Start menu

  • Choose to create a new library from the pop-up window or choose File -> New. 
  • Give your library a name (or leave it with the default name of My EndNote Library.enl) and save it
  • You will now have an empty library
  • Remember to make a back-up of your library.


Manually adding references

You can add references manually to EndNote by choosing File > New Reference or by using the New References button. New reference icon Remember to choose the Reference Type (e.g. book) and to enter each author on a new line.

Exporting references from databases - direct export plug-in

The EndNote Online direct export plug-in makes it easy to export references directly into your EndNote library from databases. The plug-in will be installed on centrally managed PC labs and should be part of the EndNote desktop default installation.

If needed, you can download it from EndNote Online ->Downloads.  You need to choose to open files rather than save.

Instructions may vary from database to database but generally you will:

  • Carry out a search
  • Mark some records by checking the boxes next to your results or adding them to a marked list
  • Choose to Export or Send to:
  • Choose RIS if you need to specify an export format
  • Open the file and you can then choose the destination for your references: EndNote (desktop) or EndNote Online

Choose Destination box

Exporting references from databases - direct export

Some databases have an EndNote button (e.g. Web of Science)  or direct export option (e.g. EBSCOhost databases) that allows you to directly export references to your EndNote library. 

For example, if using Web of Science: Web of Science

  • Search the database as normal
  • Mark the records you wish to exportWeb of Science Save to EndNote desktop
  • Use the drop-down menu to Save to EndNote desktop
  • EndNote will temporarily store imported references in a folder named Imported References, but they will also appear under All References

Importing references

If your resutls cannot be directly exported into EndNote, you can save your results as a .ris or .txt file and import the file into your EndNote library.

  • At the results page of your database search, select the article(s) you want to export and Save them as a file to your H: drive
  • Open your EndNote library and click on File > Import > File
  • Click on Choose then navigate to your .txt file
  • Click on Open to select it
  • Set the import option to either Reference Manager (RIS) for .ris files or EndNote Import for .txt files and click on Import

Your chosen results will now appear in your EndNote library.

Importing PDF files

You can import a single PDF or  folder of existing PDFs into EndNote and EndNote will create references from them if possible.

  • Go to File > Import > Folder (File for a single PDF)
  • Use the Choose button to navigate to the appropriate folder and click on OK
  • Ensure the Import Option is set to PDF and click on Import

If you have a large number of PDFs the import process may take some time.

Please note this feature is dependent on each PDF including full DOI information.

Where the process has been successful you will see your PDFs attached to automatically-generated references. Where the process hasn't worked (as in the top two references pictured below) your PDF will be attached to an empty record. You will need to double-click to open this record and type in the details manually.

Importing a folder of references

Finding full text

EndNote can  automatically locate and download full text files by accessing several sources, including: DOI (Digital Object Identifier), PubMed LinkOut, and ISI Web of Science Full Text Links. You will need to set up full text preferences first. It is also important that you select a single reference or group of references rather than the whole Library, to avoid triggering a publisher block due to excessive downloading.

To set up full text preferences:

  1. Choose Edit -> Preferences -> Find Full Text.
  2. Check the boxes next to Web of Science Full Text Links, DOI and  PubMed LinkOut
  3. Enter the following URL in the OpenURL path box:
  4. Enter the following URL in the Authenticate with box:

After setting up full text preferences:

  1. Select a reference or a group of references.
  2. Choose References -> Find Full Text.
  3. Enter your DS username and password if prompted.



Unwanted references?

After importing references into EndNote you may not want to keep them all - you may decide some aren't relevant, etc.

To remove a reference:

Highlight > right click > Move references to trash

Exporting to Excel

You can references to an Excel spreadsheet by following the instructions in this article: