Changes to EndNote with Version X4

April 28, 2011 at 3:40 pm

EndNote was recently upgraded throughout the institution to a new version: EndNote X4. Though there are many similarities between EndNote X and X4 (and even more if you used X2 or X3 in between), there are several new features and challenges to using the new version.


The biggest difference between EndNote X and EndNote X4 is the new groups feature. Groups enable you to better organize your EndNote library, particularly if you are someone who prefers to keep all EndNote references in one place.

EndNote X4 with groups pane, compared to EndNote X

There are three groups features you may wish to use: Group Sets, Custom Groups, and Smart Groups. Group Sets are a way to organize multiple groups under a single header. Custom Groups are collections of references that you choose; you must manually add references. Smart Groups are based on searches of your choosing. Smart Groups will automatically update whenever new references matching the search criteria are added to your library. In the image below, the red arrow is pointing a the Group Set name, the green arrow at the Smart Group, and the blue arrow at a Custom Group.

Group Sets, Custom Groups, and Smart Groups

To Use Groups (See the Video Below):

  • In the new Groups menu, choose Create Group Set to create a new header for a collection of groups
  • To create a Smart Group, choose Create Smart Group from the Groups menu. Search for any term or combination of terms of your choosing, and name the Smart Group whatever you wish
  • To create a new Custom Group, select one or more citations. Right-click (or use the Groups menu) and choose Add References to > Create Custom Group.
  • To add more references to a Custom Group, drag and drop selected citations onto your Custom Group, or right-click, choose Add References to, and pick the correct group
  • To see the references in a specific group, click on the group name

“Integrated Library and Online Search” Versus “Online Search” Mode

One of the biggest headaches for new EndNote X4 users is that, by default, all online searches done within EndNote automatically get added into your EndNote library. The reason for this is the new Integrated Library and Online Search mode. If you prefer the old method of completing an online search within EndNote and then picking which results to add to your library, there is an easy way to do it. Simply click on the Online Search Mode button.

Click the Online Search Mode button to put search results in a Temporary Library

Conducting an online search is a little different now, too. Just click on any online search tool in the left-hand pane to begin a search, or click on the More link to open the full list of search options. Use the search box on the bottom right of the EndNote library to search the online database.

Searching PubMed within EndNote

To add selected references to an EndNote library, highlight the references you wish to move. Right-click or go to the References menu, and select Copy References to. You will be prompted to copy the references to a new library, any current open libraries, or to select another library.

Importing PDF’s and Folders of PDF’s

Many newer bibliographic management tools, like Zotero, Mendeley, and Papers, allowed users to import a PDF’s or multiple PDF’s and would automatically find the matching citation information for those PDF’s. EndNote has joined that club.

In the past, EndNote users had to do create EndNote records before adding PDF’s, either by searching within EndNote, importing citations from a database or web site, or manually entering citations.

How to do it (see also the video above):

  • In EndNote, go to File > Import
  • Depending on whether you wish to import a single PDF file or a whole folder of files, select File or Folder accordingly
  • Choose the file or folder you wish to import. NOTE: This will only work for PDF files downloaded from publisher web sites, not scanned articles. EndNote needs to be able to detect a DOI number to correctly import reference information
  • For Import Option, choose PDF
  • Wait while EndNote imports your PDF’s. NOTE: Any PDF’s that EndNote cannot identify from DOI number will be imported as blank records or with only the file name as a title.

Importing a folder of PDF files

New Places for Custom Filters, Styles, and Connections

If you’re an EndNote power user, you may have created your own filters, styles, or connection files, or edited some of EndNote’s existing ones. In EndNote X4, instead of saving these files in the Program Files folder with the EndNote filters, styles, and connections built into the EndNote database, EndNote X4 will store any of your custom creations in your personal folders. It’s a security measure designed to prevent updates to EndNote from overwriting any custom filters, styles, or connections you’ve made, plus a way for people without administrative privileges on their work computers to edit these files. The default storage places for Windows XP are:

C:\Documents and Settings\[LANID]\My Documents\EndNote\Styles
C:\Documents and Settings\[LANID]\My Documents\EndNote\Filters
C:\Documents and Settings\[LANID]\My Documents\EndNote\Connections

If you don’t want to have your changes stored there, you can go to Edit > Preferences > Folder Locations and choose a new spot. We suggest backing up any custom files you make as well.
Want more help using EndNote? Check out the Libraries’ EndNote guide.

Melissa Rethlefsen
Learning Resource Center

Entry filed under: Feature Articles, Video Tutorials.

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