How to obtain, set up, and use Endnote to manage citations

In this Guide:

Endnote is citation management software

Endnote lets you:

Endnote Desktop:  Client Version

Endnote Basic: Online Version

  • Store, manage & format bibliographic citations
  • Easily print a list of citations & use the “Cite While You Write” feature to format citations in Word
  • Two Versions:
  • Requires purchase and installation of software


  • Requires online registration
  • Also good for downloading citations when you are away from your desktop computer, or for sharing citations within a group
  • Part of the Web of Science database, but can be used with most article databases
  • Best option for most undergrads

Endnote uses libraries to store your references. Create libraries using the steps below. For help, see: Endnote Online User Guide


1. Open Endnote:

  • Double-click on the Endnote icon
  • Or go to:  Start –>  Programs  –> Endnote
  • The Welcome To Endnote dialog box will appear  (If it does not, from the top toolbar, click HELP: Welcome To Endnote)
    • The popup window  gives an brief overview & links to help

2. How To Create or Open A Library

  • Create A New Library:   Click File NEW
  • Open An Existing Library:  Click File OPEN LIBRARY  (or OPEN RECENT,  or OPEN SHARED LIBRARY)

Parts of An Endnote Library


You have some control over how Endnote displays,
the default value is for your libraries to display as three areas or panels:

  • Groups Panel: default setting: it appears on the far left.
    • Displays any groups you have created.
  • Reference List Panel: default setting: it appears in the middle.
    • References:  Each line in this panel is an individual reference (citation).
      • To see the record for a reference, double-click on a reference  (GEAR icon in upper right: use to show/not show empty fields)
    • Column Headings: Click on any column heading to sort the citations in that library by that field.
      • Click, hold & drag a column heading to change the location of the column.
    • Fields Displayed: You can determine the fields which display in the Reference List Panel
      • Hover cursor over column heading for any field, right-click: check the fields you want to appear.
      • OR, from top tool bar, choose EDIT -> Preferences -> Display Fields
  • Tabs Panel (or Reference Panel):  default setting: it appears on the far right, can also be moved to the bottom of the screen.
    • Click on the appropriate button to display either:
      • Reference: The full record or each reference
      • Preview: Shows how the citation for a given reference will look, in the currently selected output style.
      • Attached PDFs: The PDF for the reference, if attached.
      • Paper Clip ICON: Use to link the citation to a file (usually a PDF) on your computer.
        • To delete links:  Open the reference and delete the link given in the File Attachments field.
  • Control Panel Layout:  Displays or hides the Groups Panel and Tabs/Reference Panel; controls placement of Tabs/Reference Panel  (right side, or bottom).
  • Add Output Styles:  Use to add additional Output Styles (citation formats).
    • In the Output Style Box:
      • Select the style you want to add
      • Click the CHOOSE button
      • Repeat process to add all the Style Formats you need
    • An output style is a citation format, there are hundreds (possibly thousands) to choose from.
    • Most journals have their own specific citation format.
    • Generally, you will you add the Output Styles needed for your discipline after install Endnote. Then you are done.
    • The currently selected output style shows in the Output Style window.

Safeguard your EndNote libraries and documents created with EndNote

  • EndNote libraries should always be kept on your hard drive.
  • Every EndNote library is made up of two parts, the .enl file and the .data folder. Always keep them together.
  • Back up your EndNote libraries frequently. 
    FILE >> COMPRESSED LIBRARY  will create backups for most libraries in minutes.
  • Always save Word documents (with Endnote formatting) as Word documents, and open them in Word.
    Field codes used to manage Endnote citations may be corrupted if you do not.


  • Never put EndNote libraries on network drives.  This could cause corruption.
  • Never put EndNote libraries in any type of syncing drive or folder. This could cause corruption.
    This includes: Google Drive, iCloud, OneDrive, OneDrive Business, Dropbox, Google Drive, iCloud, SugarSync, Box, etc., and syncing programs such as GoodSync.
    If absolutely necessary, a read-only copy of an EndNote library could be put on a network drive
From: The Care and Feeding of Healthy Endnote Libraries

Endnote allows you to view and set preferences for many of the program’s features.  Review your options here to ensure you are using Endnote efficiently.
See below for how to configure Endnote to Find Full Text (using UCD-eLinks or UC-eLinks).    Other changes are optional.

To view and change preferences, in the top tool bar,

  • Click:  EDIT –> PREFERENCES    The window below will appear.


Setting Preferences in Endnote



In particular, it can be useful to look at:      I recommend making the changes highlighted below, and marked with **asterisks**

**Change Case:  Identify terms where the case should NOT be changed (for example:  DNA, rDNA, PET, VLBI).

**Change Display Fields: Tell Endnote which fields to display in the Reference Panel window.

Display Fonts:  Specify the font and size of the text displayed in Library windows.

Duplicates: Specify which fields to compare when checking for duplicate citations.

**Find Full Text:  This does NOT find all PDFs!!  (If it doesn’t work, your only option is manually add links/PDFs.) 
Configure Endnote to use UC-eLinks as shown below (increases likelihood Endnote will find full text for you):

1. Open EndNote.
2. On the top menu:
– – – PCs: Select:   Edit  | Preferences |  Find Full Text (tab)
– – – or Macs: Select: Endnote  |  Preferences |  Find Full Text
3. In the OpenURL Path text box, enter:  https://search.library.ucdavis.edu/openurl/01UCD_INST/01UCD_INST:UCD?
4. Check all 4 boxes at the top.
5. Check the box at the bottom that says: “Automatically invoke Find Full Text on newly-imported references”.
6. Click OK.

Note: the OpenURL Path changed when we switched to UCD-eLinks.
The previous path may still be useful, and was: http://ucelinks.cdlib.org:8888/sfx_local

Folder Locations:  Specify location that style, filter, & connection files are stored.

Formatting:   Control formatting of bibliography entries in a word processor
and whether Endnote automatically omits duplicate references.

Libraries:  Specify the action Endnote should take when program is started:

open most recently used library
open a specific library
ask which library to open
do not open a library

**PDF Handling:  Choose:

automatic renaming options for PDFs
Choose a preset option or use custom to create your own

Specify a folder to use for PDFs that are automatically imported
Endnote will (attempt to) automatically create citations and add them to your library

Read/Unread:  Set options for the Read/Unread button:  Mark as read upon:

viewing a reference in a stand-alone Reference Window
viewing a reference within the Reference, PDF, or Preview Panes in the Library window
when the rating is changed by you

Reference Types:  Set default reference type.

Sorting: Identify words Endnote should ignore when sorting records  (default is:  a, an, the).

Spell Check:  Specify various options for Spell checking

Sync:  Allows you to add your Endnote Web credentials, and specify how to sync with your Endnote Web Account

Temporary Citations:  Do NOT make changes unless you know what you are doing.  Changes here will affect your ability to use Endnote with Word (Cite While You Write).

Term Lists: Specify how Endnote should update Term Lists.

URLs & Links:  Specify how Endnote deals with URLs and links.

Endnote recommends you keep all of your references in a single library and use Groups to manage them.

Types of groups available in Endnote, are listed below.
Groups that can be created by the user are indicated below.


Groups are displayed in the Groups Panel (shown below, in Endnote it displays on the far left).

A Group is simply a subset of references that already exist in your library.
Some are generated automatically (either permanently or temporarily) by Endnote.

Endnote Groups Panel

Permanent Groups:      Automatically generated, cannot be removed. 

• All References:    displays every reference in the library
• Unfiled:              references not part of a custom group (and, optionally, smart groups).
• Trash:                references removed from the library, will be permanently deleted when trash is emptied


Temporary Groups:    Automatically generated by Endnote; may be replaced as you use commands. 
                                 Temporary groups are always deleted when you close a library, but the references remain
                                 in your library and are not deleted. 

• Copied References
• Duplicate References
• Imported References
• Search Results
• Find Full Text


Custom Groups    (can be created by user)

• Manually created by the user to help organize your library; you can drag-and-drop to copy individual references into a custom group.
• Are listed alphabetically (click the My Library header to toggle between ascending and descending order).


Smart Groups    (can be created by user)

• Specify search criteria for group membership.
· e.g., published in journal xx, or year yy, title or abstract contains a given word, authored by, etc.
• Smart groups is dynamically updated as existing references are edited or new references are added to the library.


Combination Groups    (can be created by user)

• Use combination groups to better organize your EndNote references.
• Combine groups and use AND, OR, and NOT to create new, useful smart group sets.
• Save references in groups and then save sets of groups in group sets.
• You can collect both custom groups and smart groups within the same combination group set.

Online Search Groups

• Created when you search databases from within Endnote
(generally not recommended, few databases are available, with limited options)

Journal Term List

Some citation formats use abbreviated journal titles rather than the full journal title.
Endnote uses Journal Term Lists to substitute abbreviated journal titles for full journal titles.


Follow the two steps below to:

1) import a term list;

2) modify the Output Style of your choice to use it.

For help, see:  Journal Names:  How to set Endnote to use Journal Abbreviations     (4.5 minute video)


STEP 1. Import and Edit the Journal Term List

The Term List allows Endnote to substitute the abbreviated title for the full journal title. 
This step creates the journal term list you need.

In Endnote, select:

Tools > Open Term Lists > Journals Term List   (see image beloow)


Endnote:  Open Journals Term List


If Journals are already present in the list:

delete them (some may have info in wrong column)
To do this:  Select all journals, then click  DELETE TERM


Next, Select LISTS tab   (see image below)

Choose the  file appropriate to your discipline,
Click OPEN
Click the OK button

Endnote:  Import Journals Term List


The list you imported may not have all the journals you want.

You can update the list to add additional journal titles
You can edit the list to modify journal names/abbreviations already present


To Update the List:

Click OK button


To Edit the List:   (see image below)

Select TERMS tab: You will see a list of full journal names and their abbreviations
If information is missing or incorrect, edit or add it here

Select the journal you want to edit
Click on EDIT TERM button, correct each field, and hit OK

If you are not sure of the appropriate journal abbreviation for Chemistry journals,
Use CASSI (CAS Source Index Search Tool) to find the correct abbreviation


Editing the Journals Term List


STEP 2. Modify The Output Style So The Abbreviated Journal Name Is Used:

Select the Output Style you want to modify so journal abbreviations are used.

Edit > Output Styles > Name of Style you want to edit.
If the Output Style you want is not shown, select OPEN STYLE MANAGER and select it from there.


Select JOURNAL NAMES at the far left.   (see image below)

Under “Journal Name Format” select the field you want used, usually this will be “Abbreviation 1”
Save the output style with a new name

Finally: add the new output style you created to the Output Style Window, select it and journals titles should display as abbreviations.

Modifying the Output Style


Endnote Online User Guides
     (for both Windows & Mac)

Endnote X8
Endnote X7
Endnote X6


Endnote Training Youtube Channel

Short and long “how to” videos,
Online classes and recordings of online classes (taught by Endnote)


Training From Endnote

Videos, PDFs, online classes taught by Endnote



Seven  Ways to Get References into Endnote:

Exact steps for vary for each article database.
Article Database Directions for Citation Export to Endnote are given here:     Windows       Macintosh

For additional help see:  Getting Started Guide, Chapter 7, “Importing Reference Data Into Endnote”
Examples of for the various methods are given below.


1.  Direct Export from an Article Database

For databases that allow Direct Export (most major article databases do)

Steps vary, specific instructions for each article database are here, for:     Windows       Macintosh

General Procedure is this:    For help, see video:   Direct Export from Web of Science 

Conduct your search

From the results page: select citations to export

Click on Export/Save/etc.

Choose ENDNOTE if given the option

Select record content to send (i.e., which fields to export: Author, Title, Source, and Abstract)

Click SEND

Export typically happens automatically, you may be asked which program to use, choose Endnote.


 2. Import Citation Data from PDFs

For help, see video:  Importing [Citation Data from] PDFs

NOTE: This only works for “recent” PDFs which provide the metadata Endnote need to derive the citation information.
If the procedure does not work, your only option is to chose another method to import the citation.

References imported this way are not as data rich, as those obtained from a database.  You typically only get these fields: article title, journal or series title, author, volume, issue, page, year.


Import Citation Data from PDFs

In Endnote:  Select FILE –> IMPORT

Choose:  FILE         to import a single PDF
Choose:  FOLDER   to import all PDFs in a folder

IMPORT FOLDER:       Enter folder location or CHOOSE button to navigate to it
Click IMPORT button

If the PDF’s contain the required info, Endnote will import the citation information (required info: DOI with metadata available thru CrossRef)

If not, the import will fail and you need to use another method


3. Create An Auto-Import Folder

For help, see video:  Create an Auto-Import Folder


Create a folder on your computer for PDFs; then enable the Endnote PDF Auto Import feature.
When you do this: Endnote will attempt to automatically import citation data and PDFs to your Endnote library.

Again, this only works if the DOI is embedded in the PDF metadata.
If you already have a citation in your Endnote library, and add PDF for it, Endnote tries to recognize that and attach the PDF to the existing citation.


On Your Computer:

Create a folder for PDFs, save it in convenient place (i.e., desktop).
Name of folder does not matter.

In Endnote:

Select EDIT –>   PREFERENCES  –>  PDF Handling

Under PDF Auto Import Folder:
SELECT the folder you created

If the PDF’s contain the required info, Endnote will import the citation information (required info: DOI with metadata available thru CrossRef)

If not, the import will fail and you need to use another method


4. Add Directly From Publisher Website


Many publishers allow you to add citations to Endnote directly from their websites
(See:  ACS JournalsRSC JournalsElsevier (aka ScienceDirect), ScienceNature,  etc.)

Look for links that say: Download Citations, Export Citations, etc.
Usually you will need to select Endnote and specify whether you want the citation only, or citation and abstract


5. Save as Text File in Article Database and Import to Endnote  (Two Step Process)


Most databases (including PubMed) now allow direct export (see #1).
To illustrate how this process works, instructions for importing a text file from PubMed are given below.

Database specific instructions are given here for:     Windows       Macintosh


Save as Text File and Import:  using PubMed as an example

Step 1: Conduct your search in Pubmed (or another database)

Select citations to export (usually by checking a box)

Click SEND TO link  (upper right of results list)

Choose FILE

Then for FORMAT, choose: MEDLINE

The SORT BY field, you can ignore



Step 2: Import Citations Into Endnote

Open Endnote

Open the Endnote library where you want the citations imported

Select FILE -> IMPORT -> FILE, and enter:

Import File:  Enter name of file

Import Option:  PubMed  (NLM)   [Enter correct option for the database you are using]



6.  Google Scholar: How to Add References to Endnote

(Probably not your best option: citation records will be minimal)


Step 1: First configure Google Scholar as shown below:

Go to the Google Scholar home page at http://scholar.google.com

Click on the SETTINGS link.

Click on SEARCH RESULTS (left side of screen).

Under Bibliography Manager, select: “Show Links To Import Citations Into ENDNOTE”

Click SAVE


Step 2: To import citations from Google Scholar into Endnote:

Search on Google Scholar

Click on the IMPORT INTO ENDNOTE link under the reference you want to import

In the next window that appears, select:  OPEN WITH  and select ENDNOTE  (navigate to it if necessary)

Click OK.


7.  Add Manually


To cut and paste, or enter citations manually:

Open Endnote
Enter info

Endnote allows you to:

• insert both in-text citations and the full reference at the end of your paper, as you write
• format citations in any style you wish
• change the formatting of citations, at any time, with just a few simple clicks

A quick overview is below. For more information refer to the help section on this guide. 
For additional help see:  Getting Started Guide, Chapter 8, “Using Endnote While Writing A Paper in Microsoft Word”
and:  Cite While You Write: Adding Citations to a Word Document


You need to have Word and Endnote installed on your computer, and have the citations you want to use in your Endnote library.


Steps for using Endnote with Word: 


1. Open Endnote and the Endnote library containing the references you want to use.


2. Open a document in Word and bring up the Endnote toolbar.

• For Word 2010: click on ENDNOTE X6 tab.


3. Use the OUTPUT STYLE window to select the citation format you wish to use (see image above).

• If the style you want is not listed, click on the dropdown arrow:
• choose SELECT ANOTHER STYLE,  pick the style you want, and click OK.
• For more help: see “Add Output Styles” on Endnote Libraries Tab


4.  Place cursor where you want in-text citation to appear.


5. Click INSERT CITATION icon in the Endnote X6 Toolbar (or FIND CITATION icon in older versions of Word).

• Select the citation(s) you want to insert
• Click INSERT.

Endnote will insert both in-text citations, and full citations at the end of your paper.


6. Keep writing.  Repeat steps 4-5 until your paper is complete.


7. If you want to change the citation style used in your paper at any time:

• Go to the OUTPUT STYLE window on the Endnote X6 toolbar:
• Click on the dropdown arrow.

• The Output Styles listed ared those you have previously selected.
• Select the new Output Style.

If the style you want is not listed:
• Choose SELECT ANOTHER STYLE,  pick the style you want, and click OK.

Both the in-text citations and the reference list at the end of your paper will be changed to the new style.


Two versions of Endnote are available:

this section explains web version: Endnote Online,
all other sections in this guide refer to the Desktop (Client) Version of Endnote.


Getting Started with EndNote Online


1 Collect 2 Organize 3 Format
Collect references from electronic and traditional sources.

Organize your references for your research topics and papers.

Create a formatted bibliography for your paper or cite references while you write.


Endnote Online


1.  Register for an account


2.  Getting References INTO Endnote    


from Web of Science:

• Log on to Endnote Web
• Search Web of Science, from the Web of Science results screen

• select citations to export

• click on the Save to Endnote radio button
choose Save to Endnote ONLINE

• select record format to send, choose:   (Author, Title, Source, and Abstract)
• click SEND

• Export will happen automatically


from  SciFinder:

• Select citations to export (use checkboxes)
• Click EXPORT  (near top right)
• Choose TAGGED FORMAT (*.txt)
• Name it or note the name of the file
• Log on to Endnote Web
• Select COLLECT tab
• Enter:

• File:  Enter name of file
• Import option:  SciFinder (CAS)
• To:  Select group (library) where citations should be imported

• Click IMPORT
• You can also cut and paste, or enter citations manually



3. Create Libraries (two methods)


• New Group



• Select references for new library
• ADD TO GROUP –> New Group



4. Getting References OUT of Endnote

  • Create List of References:
    • References: choose library
    • Bibliographic Style: choose citation style
    • File Format: choose RTF
    • Select  FORMAT tab
    • Choose:  SAVE, EMAIL or Preview & Print
  • Cite While You Write
    • Let’s you embed citations in your Word document, while using Endnote Web to format them
    • For help, see: Endnote Online User Guide


5. Sharing References

Allows you to share references with others

• Manage My Groups
• Manage Sharing

• Add email(s)