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EndNote Guide: Manage References

With EndNote you can customize the program and your Libraries by changing the default options under Preferences (Edit on the PC and EndNote on the Mac).  See details under Install & Backup: Basic settings tab

You may want to consider altering the following:

  • Find Full Text -- uncheck Automatically invoke Find Full Text on newly imported references
  • Libraries -- set the default which Library opens when you launch EndNote
  • PDF Handling -- opt to create a watched folder
  • Read/Unread -- you can select when the button changes from Unread to Read
  • Sync -- enable Sync feature with EndNote Online

Editing a Record

To view the complete entry for an individual record in your library, double click on the reference. With the reference window open you can edit fields; you will be prompted to Save your changes.

  1. Use the Tab key to move from field to field.
  2. Within the reference window, use the gear icon to hide or show empty fields. This helpful feature reduces the need to scroll through vacant fields.
  3. If a PDF has been attached, the document will appear in a separate frame. You can email, highlight, or make notes to the PDF. Your changes will be saved in the library.

Selecting a Layout

EndNote offers different layout options for how you view your Library. The layout options vary slightly from the PC and Mac versions.

  • Click the Layout icon (Windowns, bottom right; Mac, upper right) to select how you want to view your EndNote Library. Note: A popular layout is Left panel; Bottom Right.


Within the Library, you can click on a displayed Field (e.g., Author, Year, Title, etc.) to change the sort.

  • For example, it can be helpful to sort by year with the most current references on top. Or, you may want to see your library sorted by author to identify researchers that have written extensively on the topic.

The search function in EndNote allows you to locate references within your library. This is an especially helpful feature if your library is very large.

  1. From Tools select Search Library. You can search any fields using the operators OR, AND, and NOT. Note: You may also do a Quick Search using the Search Library box.

Searching Tips

  1. Search Whole Library or Specific Groups: You can elect to search your entire Library or within a specific Group.
  2. Search within a specific field, e.g., Title, PDF, etc., or use a combination of fields.
  3. Author Searching: An author search with this function will find authors who are not displayed as the primary author. An alternative author field is "First Author."
  4. You can convert a search to a Smart Group (with each import of new records, records that match the search will show up in the group). To do this, click on the gear icon and select Convert to Smart Group. In the "Converted Search" box, enter a group name.

EndNote files can be difficult to transport (e.g., email) due to their size and easy-to-lose supporting files. You may solve both problems by saving your file as a Compressed Library. This single file can be attached to an email, saved to USB drive, or uploaded to the Cloud (e.g., Google Drive).

  1. To save a compressed copy of a library, go to File and select Compressed Library (.enlx)
    • The EndNote library will have an .enlx extension. The compressed library is opened automatically by EndNote by just clicking the file icon.
    • Select With File Attachments to include PDFs and other attachments.
    • You may select if you want to compress All References in Library, Selected Reference(s), or All References in Group/Group Set.
  2. Click OK and enter a filename, e.g., My Library Sep 12.
  3. Important: Once you click on the .enlx file, EndNote will automatically open and create two files, a .enl and .data file. It is recommended that you delete the downloaded .enlx file -- everytime you click on this .enlx file, it will create a new copy which can be very confusing.

EndNote will search for updated reference information for existing records. This feature is particularly helpful if you transferred records from earlier versions of EndNote that are missing PMCID or NIHMSID numbers. It is also useful when authors are using e-pub ahead of print citations.

To use this feature:

  1. Highlight the record(s) you would like to search for updates on, click References, and select Find Reference Updates.
    • Alternatively, right-click and select Find Reference Updates.
  2. As databases may be updated periodically, you may want to try this feature again at a later date if the expected updates are not available.
  3. If an update is found, you will be prompted to review which fields have been updated to compare to the current record. You may select to Update All Fields or Update Empty Fields.
  4. If you want to move to the next record without making any changes, click Skip.
Create a Group

Organizing references into Groups or Group Sets makes it easy to break a large library into subsets. A group simply points to a subset of references that already exist in the library. Groups may be organized into “sets” of groups and “smart groups.” Finally, you may combine groups using the Boolean concepts of AND, OR, and NOT.

Groups feature allows you to define your own set of handpicked citations – organize your library by theme, the project you’ll use the citations for, the items you’ll need to order, etc.

To create a group(s):

  1. Right-click on My Groups (left panel), select Create Group, and enter a name for the group. Alternatively, select Groups from the menu bar and then Create Group.
  2. To move a citation or set of citations into a Group, start from “All References” and drag and drop highlighted items from your reference window onto the group’s name.
    • A citation can be added to multiple groups.
    • If you delete a citation from “All References,“ it will also be deleted from the Group(s).
  3. To remove a citation from a group, highlight the citation(s), click Groups, and select Remove References from Group.
    • Alternatively, right-click on selected citation(s) and select Remove References from Group or just press Delete key.

Create a Group Set

Group Sets allow you to create “groups of groups.” This may be useful to organize groups into different categories. For example, a group called “Databases” differentiates the results from CINAHL, PsycINFO, and PubMed search from the results.

  1. Right-click on Groups, select Create Group Set, and name your set.
  2. To create groups within the “group set”, simply click on the Group Set and right-click to Create Group.

You may often wish to pool the contents of individual groups. Groups can be combined using the Boolean operators of AND, OR, and NOT.

  1. From the Groups panel, right click in the section you’d like to have a combination group. Right-click to select Create from Groups. Or, References and select Create From Groups.
    • In the Create From Groups box, select which groups you wish to combine and how you wish to combine them (e.g., AND, OR).
  2. The resulting group will have an icon that looks like three intersecting colored circles.

Smart Groups are much like persistent search results. Create a smart group based on a particular field (e.g., Author contains Jones), and Endnote will automatically populate the smart group with every record that matches your criteria. To create Smart Groups:

  • From Groups select Create Smart Group to open the Smart Group box. Alternatively, right-click on or under My Groups and select Create Smart Group.
  • Provide a name for the Smart Group and enter terms to define the search.

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