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Introduction to EndNote x8 and EndNote Online

EndNote Desktop X9


Click on the individual tabs above to learn more about managing your EndNote library. 

Navigating your Library

Groups panel - this is where all your groups - i.e. folders live

Search panel - use this function to search within your reference library, and to search databases from within EndNote

Reference panel - on the right hand side of the screen; gives you access to a number of tabs: 

Reference - shows the detailed record for the reference you have selected in the reference list panel. Information in this panel can be edited. 

Preview - shows the highlighted reference formatted according to the selected reference style, e.g. Harvard. 

Attached PDFs - may contain a full-text PDF of the item, if one was imported. You can add sticky notes to your PDFs in this panel. 

Reference list panel - shows reference ID numbers, authors and titles of entries in your EndNote library. The display can be customised to show additional information fields, e.g. journal title, year of publication, etc. The default reference list sort option is alphabetically by author. References can be sorted by any of the columns shown in this pane, i.e. clicking on the Title heading will sort references alphabetically by title. 

Panel Layout - the reference panel can be moved or hidden from the layout menu button in the bottom right corner of the window.

Organising with Groups

Permanent Groups

EndNote's folder systems are called "Groups". You can create "groups" and "smart groups" to help you organise your references.

Some groups are automatically added to your EndNote library, and cannot be deleted. For example, the "All References", "Search Results", "Unfiled" and "Trash" groups. 

Temporary Groups

Temporary groups appear in your library when you perform certain searches or actions, for example importing references, or searching within your library.

These groups will only remain in the "All References" group for the duration of the time you're working in your library. 


Groups work the same as folders, and allow you to organise your references by topic or specific criteria.

If you don't assign a reference to a group it will appear in the "unfiled" group. References can be filed in multiple groups. 

To create a group and add references:

  • Go to the "Groups" tab and click "create group"

  • Name your Group 

  • To add references simply highlight the references you would like to add, and drag and drop into your chosen group. 

Smart Groups

Smart Groups are like saved searches.

They are created by specifying inclusion criteria at the time of creation, and any reference that meets those criteria is automatically added to the smart group. 

To create a Smart Group:

  • Go to the "Groups" tab and click "Create Smart Group"

  • Determine your inclusion criteria in the pop-up window, and click "create"

  • Any reference that meets the inclusion criteria will now be added automatically to this Smart Group

Deleting References in Groups

References can be deleted by highlighting the reference(s) and using the delete key.

Any reference that is deleted from a group will only be removed from the group. The reference will still remain in the main library and any other groups it's filed in. However, if a reference is deleted from a Smart Group it will be deleted from the main library. 

To remove references from your library locate the reference in "All References" and delete. 

Find Full Text

You can search for open-access PDF material for your references in EndNote, using the "Find Full Text" function.

Highlight the selection of references you would like to search, and click the "Find Full Text" icon in the top menu bar (see below).

If material is found, EndNote will automatically import the PDF file and attach it to the relevant reference. You can view the PDF in the reference panel as seen below. 

Searching your Library

To search your library use the search panel fields. 

You can limit your search to a specific group by selecting the group of references in the Groups panel on the left hand side.

To search all the references in your library ensure the group "All References" is selected in the groups panel on the left hand side. 


Finding Duplicate References

Go to the "References" tab and click "Find Duplicates" 

EndNote will run a duplicate search on all the references in your library. 

If there are any matches a pop-up window will appear (see screenshot below). 

You can sift through each duplicate record and select which record you would like to keep, using the "keep this record" button.  





Deleting duplicate references all at once

You can automatically delete duplicates by clicking "Skip" in the "Find Duplicates" window.

You will return to the library and a list of duplicate references will be highlighted.

To delete all hit the delete key on your keyboard.

Syncing References to EndNote Online Account

You can sync your Library across both EndNote Desktop and EndNote Online accounts, so your library always stays up to date, whether you're working offline or online. 

To sync your EndNote Desktop library with EndNote Online, click the sync button in the tools menu.

Add your EndNote Online account information into the window as prompted.

The first time you sync it may take some time to process. 

EndNote Online (Basic)

Click on the individual tabs above to learn more about managing your EndNote Online (Basic) library. 

Navigating your Library

  1. My References - view your references in your library and your groups/folders
  2. Collect -  add a reference manually, import a reference file, or search a database from within EndNote
  3. Organize - create, re-name and re-order your groups, find duplicate references, manage PDF attachments
  4. Format - email or print a formatted bibliography of your library, download the Cite While You Write plug-in, export references in a reference style of your choosing
  5. Match - a journal-matching tool to help researchers find a suitable journal to submit a paper to
  6. Options - edit account information
  7. Downloads - download plug-in software e.g. Cite While You Write and the Capture Reference tool 

My References

In My References you can view, search, sort, delete, group and edit your references.

Searching - Use the free text search box under "Quick Search" to search within your references. 

Sorting - You can sort your reference list alphabetically, by author, year, citation, etc using the the dropdown menu on the right hand side. 

Deleting - You can add and retrieve references from the "Trash". To delete a reference or multiple references, pre-select them and click "delete" to add them to "Trash". To retrieve references from the trash, click on "Trash" and select the reference or references you would like to add back to your library. In the "add to groups" dropdown menu select the group you want to add the reference to.  

Editing - To edit or read references individually, click on the title information of the reference you wish to read. To edit your reference, click anywhere within the reference to begin typing/editing. 

Grouping - You can organise your references into "groups", which are the same as folders. To add a reference or multiple references to a group, pre-select them and click on the dropdown menu "add to group" to select the group you would like to add them to.

Managing your groups

You can manage your groups in the "Organize" tab, using the "New Group", "Managing Sharing", "Rename", and "Delete" buttons.


Finding Duplicates

You can remove duplicate references from your library in the "Organize" menu, under the "Find Duplicates" tab.

EndNote will automatically scan your reference library for any duplications, and highlight any it finds.

The duplicate references will be pre-selected (see screenshot below) in order for you to delete them all at once, by clicking the "delete" button.  

The references will then be removed from your library and added to the "Trash". You can retrieve deleted references from the trash if needed.