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Citation Management Tools: EndNote

A quick guide to using citation management tools.

What is EndNote?

EndNote is a reference and full-text organizer that lets users create formatted citations and bibliographies, or independent reference lists. There are a number of versions available for purchase, the current being EndNote 20. Students can purchase EndNote 20 for $115.95 with proof of enrollment. This is available for both Mac and PC, and includes the EndNote X9 software download and access to EndNote Online with unlimited file storage, unlimited reference storage, and group sharing.

EndNote Basic is a free cloud version of EndNote. Since it's free, it does have limited storage space and less functionality than the full version of EndNote. 

Basic works well for students with smaller scale research needs. Free accounts come with space for up to 50,000 references and 2GB of stored attachments. Keep in mind this is cloud storage as Basic does not include a desktop app. This means you can access your citations and attachments from any computer that has internet access, but it is not automatically saved to your device. 

**KCU has EndNote available to faculty and staff, but not students. Students who wish to use EndNote will need to purchase it for themselves, or use EndNote Basic for free.**

EndNote Basic

To get started, visit create your free account. 

The quickest way to learn about the features on EndNote Basic is through the Getting Started Guide. Be sure to check out all the features before you start downloading citations. If it isn't shown on your screen when you first login, you can find a link to the Getting Started Guide on the upper right portion of your screen.

There are 3 options for collecting resources: Online, New Reference, and Import Reference. 

Online search lets you create a search and pull citations from certain databases and library catalogs. To start, select where you want to search from the dropdown menu (PubMed(NLM)) will be the most useful.). Click Connect

In the search boxes, enter your terms and select a field (use any field to search all fields). For searching using multiple terms, use the Boolean Operators in the dropdown menus on the right. Click search. 

To select citations to save, click the checkboxes next to the citation and select a folder from the Add to Folder dropdown menu. 










Adding a New Reference is the manual option for adding citations. Simply fill out the form with the correct information and click save when you're done. This will add the reference to your list. 

Importing citations to EndNote Basic is similar to other citation manager imports. First, select the file that contains your citations (typically in .nbib, RIS, ect formats). Select your import option, PubMed being the easiest. Select the group you wish to import to, use Unfilled if you don't have groups.



You can also use the Capture Tool. Check out the directions below under EndNote X8 Importing.

The Format tab helps users create bibliographies, format papers, export references, and contains the Cite While You Write™ Plug-in. 

Bibliography: create quick bibliographies from the citations you've stored in EndNote Basic. Select the references from your library through the dropdown menu. Choose a bibliographic style **Note that AMA is not an option**  Select the file format. You can save, email, or preview and print your citations. 

Format Paper: Upload your paper in .rtf (Rich Text Format). Choose your bibliographic style and click Format. 

Export References: First, select the reference list you want to use from the References dropdown menu. Next, choose the export style you want. You can then save, email, or print your references. 

Match is a neat tool for authors that analyzes data points and citations connections from the Web of Science to help identify meaningful relationships between publications and the citation information for your own article. 

To find journals that your paper would fit in, enter your title and abstract into the designated boxes and Click Find Journals>

EndNote X8

KCU Faculty and Staff can request EndNote X8 be downloaded to their KCU owned computer. We do not provide access to EndNote to students, but it is available to purchase. 

Once EndNote has been downloaded on to your device, open it on your desktop. You will be asked to login to your EndNote account. An EndNote Online or an EndNote Basic account will work. If you don't already have an account, follow the prompts to create one. 

Important Information for Using EndNote:

  • EndNote libraries are made up of two parts: the .enl file and the .Data folder. These two parts must be kept together, both are needed for the library to work correctly.
  • EndNote libraries should be kept on your computer's hard drive. Storing and editing libraries on a network drive can lead to corruption and performance issues.
  • EndNote libraries should never be stored in cloud-syncing folders such as Dropbox, OneDrive, Box, SugarSync, etc. Syncing folders corrupt EndNote libraries over time.
  • Uninstall your previous version of EndNote before installing a new version.
  • References in EndNote libraries can be synchronized between desktop and laptop computers, the online library, and an iOS device using EndNote Sync.
  • Complete EndNote libraries can be shared with other EndNote X7, X8, or X9 users through EndNote Sync and Library Sharing.

To get started with EndNote, it's best to figure out the basic features of your EndNote Library. The top menu bar is where you'll find most of the customization areas within EndNote Library. For example, you can change the view of your Library using the Window menu. Feel free to test out the different settings to decide which works best for you. The examples below are using Tile Horizontally.

Most things within the Library are adjustable. Click and drag lets you rearrange the order of information in your Library. You can set your layout for both the Groups and Reference panels. The Rating column lets you rate your citations however you'd like; the dot indicates a citation has been opened; the paperclip indicates a PDF has been added. 

The Reference Panel is on the far right and shows more details about a selected citation. **Double clicking a reference will open it in a second window. A single click highlights the reference and opens the information in the Reference Panel.** 

The Reference tab breaks down all the citation information and for you to view and edit. 

The Preview tab uses the current output style to display the selected reference as it would be formatted for a bibliography. EndNote’s output styles (or just styles) represent the rules for creating bibliographies for a variety of journals and other publications. The styles determine how your references look when you print, export, preview, or create bibliographies. 

To select a different output style to apply to the reference, go to the main toolbar and select APA 6th (or any other citation style) from the drop-down list of output styles. 

Groups are a great way to keep track of where your reference belong and stay organized. To create groups, start in the Groups menu. Select Create Group  (Or, you could right click in the Groups panel to display a context-sensitive menu, and then select Create Group.) Name your group and click Enter. To add references to your group, highlight the reference from your library and drag it to the group. 

To delete groups, right-click the group name and select Delete Group. Deleting groups DOES NOT delete your references. 

There are 3 types of groups in EndNote:  Custom groups (manually add records to group),  Smart groups (records updated automatically by matching group's criteria), and  Combination groups (created by combining other groups).

There are 3 ways to enter references into EndNote: 

  • Manually enter reference
  • Connect to an online bibliographic database and download directly into EndNote*
  • Import text files of references*

*The next two tabs will cover the other two methods to add references.

To manually enter a reference, select New Reference (or CTRL+N) from the Reference menu. 

In the new window, select the Reference Type and then fill out the remaining information. If you have a PDF to attach to the reference, click the paperclip, select the correct file, and click Open


In order to add references through an online search, you first need to connect to the PubMed Database. 




Start by clicking the Online Search mode button on the toolbar. 



Once the Online Search screen is up, select PubMed (NLM) from the listed options. If you have not used EndNote to search online, you will not see PubMed (NLM) listed. You will need to add the connection to get started searching. To get the PubMed (NLM) connection added, click More...
Scroll down until you find PubMed (NLM) and select it. Then click Choose

While still in the Online Search screen (globe icon selected), you can begin searching. The center panel of Online Search changes from a list of the references stored in your EndNote library, to a list of references for your search. You'll also notice that the drop down menu at the top has changed to Search Remote Library, indicating you are no longer searching through your own references, but are connected to a database. 

The other drop down menus allow you to change the fields of the search. You'll see MeSH Terms highlighted in blue above, but there are many options that you can select, including PMID, Author, Journal, etc. The middle drop down will always be Contains. To the right of the search box, the plus (+) will add another row of search boxes to build on your search using Boolean Operators (AND/OR/NOT). The minus (-) will remove a row. You may have to adjust the size of the search box in order to see multiple search rows. 

Once you've built your search query, click the Search box at the top. You'll see a pop-up titled Confirm Online Search that shows a summary of the search results. Click OK to retrieve the records. 

You will begin to see references loading on the Online Search screen. Large searches may take a while to fully load. You can stop the retrieval at anytime by clicking the Cancel button (replaces the Search button while references are uploading) or by hitting the ESCAPE key (ESC).

To save a reference to your EndNote Library, hold down CTRL and click the references you wish to save. Click the Copy to Local Library button to add the references to your permanent EndNote Library.


To leave Online Search and return to your permanent library, click the Local Library button.


References copied from your Online Search will appear in a Copied References group. This is a temporary group, meaning the next time you copy a set of references from Online Search, it will replace the existing set. This set will also disappear if you close your EndNote library, so it is important to organize them before closing out EndNote. 

Online searching, described in the previous section, is one way to retrieve references from online databases, but it does not offer the advanced search capabilities that may be available from KCU's databases available through the library's website.

You will need to download the Capture Tool from EndNote online in order to import references from many databases. Importing citations from PubMed DOES NOT require using the Capture Tool. See the PubMed tab for instructions. 

To download citations: 

  • Make sure you have EndNote opened on your desktop or are logged into your Online EndNote library.
  • Go to the database/website you want to use. Perform your search like normal. When you find a citation to save, click to open the abstract.
  • Click Capture Reference in the toolbar of your browser window.

  • A temporary EndNote window will open and display information about the website.  If you are not logged onto your account, you will be prompted to do so.

  • from the pull-down menu, make sure you select the proper type of resource for which you are importing (i.e. web page, journal article, book, newspaper article, etc.).
  • In the Save To section, select where you'd like to save the citation. ( will save to your online EndNote library; EndNote option will create a text citation that you can download into your EndNote desktop library)
  • Make sure all necessary information is imported into the fields of the online form. Edit the form as needed. 
  • Click the Save button

  • When successfully imported, you will receive a the following message: The reference was captured into "[folder name]" successfully

  • If you used EndNote as your download location, a text file will be created and automatically downloaded. To use it, simply click the download to open it in your EndNote desktop. 

Another option is to find the article in PubMed and import to EndNote. Databases like Clinical Key will have a section that lists the NLM Citation ID for MEDLINE indexed articles. We usually refer to this as a PMID, meaning it's a number that is used to quickly find the citation information for this exact article within PubMed. 

If you click the link, you will be redirected to PubMed and the citation for the article. From there, you can download the citation into EndNote using the steps on the PubMed tab. 

Creating a bibliography with EndNote first requires searching for and selecting the references. 


Be sure you're in Local Library Mode and can see all your references. If not, click the file folder icon on the left of the screen. Click the All References group to search all the references in your library. 



Use the Search panel to search your library for references. Just like searching Online Databases, enter your terms, select fields, and add or subtract rows. 


Click Search. Once the search is complete, results will be displayed in the Search Results group. 

You can also use the Match Case and Match Words checkboxes to narrow your search or find specific references. 

  • Match Case: This option would limit the search to “grey parrot” in lowercase. If it were found capitalized at the beginning of a sentence, or all uppercase, it would not match the search.
  • Match Words: This option would limit matches to full words, with no truncation. 

Smart Groups are an easy way to automatically sort your search results. Converting your search into a Smart Group means it wil lbe available at all times and constantly updated. 

After creating your search criteria, click the Options button in the Search panel. Choose the Convert to Smart Group option. This will create a new smart group titled "Converted Search". You can rename this by right-clicking the group and selecting Rename Group. Press enter to save. 

Once you've gathered all the reference you need for your bibliography, you're ready to export them and edit in a word-processing program. 

  • Select all the references in the Search Results (or your Smart Group) set.
  • Select Export from the File menu.
  • Click the Desktop icon in the Export file name dialog to save the results on the desktop.

  • Name your file and change the Save as type to Rich Text Format (*.rtf). 
  • On Output style, select the citation style you need, such as APA. The drop down menu contains your favorite styles, but you can select any style installed on your computer by selecting Select another style... from the menu. 
  • Mark the box Export Selected References to export only the references you have selected in EndNote. 
  • Click Save.
  • Open your file in your word processor to see your bibliography. 

Cite While You Write™ (CWYW) is a plugin for EndNote that allows you to insert references, and format citations and bibliographies automatically while you write your papers in Microsoft Word. It also lets you save your online references to your EndNote Library. 

The CWYW feature inserts a tab with EndNote commands onto Word’s ribbon to give you direct access to your references while writing in Microsoft Word. The Cite While You Write commands enable EndNote to format the citations and bibliography of the document that is currently open in Word. 

Start by opening your EndNote desktop. Write your paper as normal. When you're ready to insert a citation:

  • Place your cursor at the end of the line you need to insert a citation.
  • Click the EndNote X8 tab
  • Click the icon for Insert Citation (click the TOP of the box, not the words)

  • The Find & Insert My References box will appear. Enter the reference you need (name, word, etc) and hit Find or Enter.

Another way to insert citations is by selecting in your EndNote library and inserting them. For this method: 

  • Place your cursor at the end of the line you wish to insert a citation after. 
  • Click EndNote X8 tab
  • Click the Go to EndNote button. This will take you to your open EndNote library. 

  • In EndNote, select your references
  • Click the small Insert References button on the toolbar. This will insert your references where you left of in word.

You may need to change your citation style in order to insert into Word with the proper format. To change just the style used for the citations and bibliography, choose a new style from the dropdown Style menu. If you do not see the style you want, click Select Another Style… to select any style installed on your computer.

If you would like to change more options than just the style, click the small arrow button on the bottom of the Bibliography group on the EndNote tab. This will open the Configure Bibliography dialog. The Configure Bibliography dialog contains many options for changing the format of the bibliography.

  • There will be two tabs in the Configure Bibliography window, Format Bibliography and Layout. From the drop-down With output style on the Format Bibliography tab, you can change the style of your bibliographies. If you don't see the style you need, click the Browse button to show a list of all styles available on your computer. 
  • The Layout tab shows different layout options for your bibliography, including changing the font or font size. You can add a title for your bibliography in the Bibliography title field. If you want to change the font for just the title, select the title, and then click the Text Format button to select a title font. To set the line spacing to double-space, select that option from the drop-down Line spacing menu. Click OK when you have finished making changes.

EndNote is a comprehensive citation management tool that offers a variety of features. We just covered the basics here, but feel free to stop by either D'Angelo or Dawson library for help. It's also important to note that this tutorial is based on EndNote for Windows and features may look different on a Mac. Below, you will find additional resources on EndNote including the EndNote X8 Quick Reference Guide for Mac:


EndNote's Capture Tool lets you capture online references. To install, drag the Capture References button on the screen to your Bookmarks bar. To use, visit a page you'd like to save and click the Capture Reference button on your bookmark bar. A popup window will open and walk you through saving the reference.

EndNote for Apple

EndNote is only available for iOS. You can download EndNote to your iPhone or iPad and have your citations on the go wherever you are. Visit the app store and download EndNote to get started. Login with your EndNote online account. 

To sync your EndNote library, click the SYNC button (red circle)

[1]-My Library; [2]-Online Search; [3]-New Reference; [4]-Downloads; [5]-Profile

EndNote Support

A big plus to using EndNote is their company support. Check out these links for help.

Other helpful EndNote links:

  • EndNote Output Styles- to update or obtain new output styles (APA, NLM, journal specific styles, etc.)
  • EndNote Import Filters- update or obtain new import filters that allow EndNote to ingest data from specfic databases (PubMed, OVID, etc.)
  • EndNote Connection Files- update or obtain new connection files. Connection files allow EndNote to search databases directly (PubMed conneciton file)
  • Software Updates- updates for specific versions of EndNote with patches, fixes, etc.
  • EndNote Templates- update or obtain journal specific templates

**If you're using EndNote Basic, the styles, filters, files, and updates will not work on your device.**

Online Help for Other EndNote Versions

*KCU faculty and staff with EndNote currently have EndNote X8