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University Library, University of Illinois at Urbana-Champaign

EndNote: Organize

An overview of EndNote bibliographic management software with detailed information on getting started and customizing your software.

Editing References

The accuracy of the references you import into EndNote is only as good as the information in the databases you took them from. Therefore, always double check your references.

Just right click on the citation you'd like to edit, and select Edit Reference.

Edit References in EndNote

Some things to watch out for:

  1. Formatting: italics, sub/super scripts, etc.
  2. Reference Type: if the wrong reference type is selected, some information may not be present.
  3. Names of journals
  4. Abbreviations, truncations

Creating Groups

EndNote allows you to organize your library into Groups (which basically work like tags or folders). For instance, if you wanted to make a Group of records for a paper you want to submit to Nature, you would follow these instructions.  You can also create smart groups, which populates a group based on a certain characteristic (such as author name, year, or other field).

1. Right click on My Groups in the left hand column, choose Create Group, and give it a meaningful name (e.g., Nature 2012)

Create a Group

2. To add records to this group, right click on the ones you want, select Add References to..., and choose the Group you just created.

Add References to a Group

Removing Duplicates

  1. To remove duplicates from an EndNote library, click on the References tab at the top, and click Find Duplicates
  2. A screen will pop up that lets you compare the duplicates side by side so you can choose which record to delete
  3. If you want to mass-deduplicate the library, by-pass the comparison window by clicking on Cancel.  You’ll now see the library with the duplicate records selected.  You can just “delete” the selected duplicates without examining them, if you like.  (Or, while holding down the Control key, choose which duplicates to select.)  Be careful not to remove records that you have edited or to which you have attached PDFs!

Adding pdfs

Pulling PDFs into EndNote from the Web using the “Find Full Text” option for a citation.

  1. This only works if you have already customized EndNote’s URLs & Links and Find Full Text (see the Getting Started tab), which are located under Edit / Preferences.
  2. Open an EndNote library
  3. Select an article (or several)
  4. Right Click / Find Full Text / Find Full Text. The first time you will be asked for a netid and password.
  5. It may take a minute or two, but eventually a “paperclip” icon will appear next to the reference.  Open the reference, scroll down to Attachments, and you will find the PDF. 

Adding PDFs already located on your computer

  1. In the File Attachments field of the EndNote record, Right click / File Attachments / Attach / [navigate to locate the file] and Open.
  2. If the PDF has a DOI and is not already in your EndNote library, EndNote will create a new citation.  Do this by going to File / Import / File with the Import Option PDF selected.

Accessing full text through the library website (Discover link)

1. Select the reference of interest in EndNote and right-click on it. Select URL and click on OpenURL Link. This takes you to the U of Illinois Library “Discover” window, from which you can choose the online version of the article

Access full text

Annotating PDF Files

When a PDF file is embedded in an EndNote record, then you can annotate it using the tools provided to highlight and comment.

Adding DOIs

If you need DOI information added to all the citations in your EndNote library, you do not have to manually search for each DOI.  Librarians at the Grainger Engineering library have a way to automate this process.

You will need to convert your library to a text-only format.   

From within EndNote, with the appropriate library open:

  • Click on:  File / Export
  • Give the output file and name, and choose a location for the file
  • Save as file type “.TXT”
  • Choose Output style RefMan (RIS) Export

Send this file to Josh Bishoff [] requesting that DOIs be added to the file.  When your library is returned, you will need to reinstall it:

From within EndNote, open the library that you exported and delete all the records:

  • Click on:  Edit / Select All
  • Click on:  Edit / Clear

Now you’re ready to re-import the records from the file that contains DOIs:

  • Click on:  File / Import / file

Locate the file that has the DOIs

  • Import Option should be set to Reference Manager (RIS)
  • Duplicates:  Import All
  • Text Translation: No translation
  • Click on Import

Your library is now restored!  If you had attachments to pdfs etc, those pointers will be maintained.