EndNote X6
What is EndNote?
EndNote is citation management software that allows you to organize and retrieve your literature references for
research, teaching and publications. It works with Microsoft Word to format bibliographies and easily enter citations
into your paper. For additional help see the Ebling Library Citation Management Portal at:
http://ebling.library.wisc.edu/portals/reference_tools/citation_styles.cfm
Endnote Desktop vs EndNote Web
Desktop
 Software is loaded on
desktop or laptop computer
 $73 from DoIT Tech Store
 Unlimited in size
 Can attach pdfs, etc.
 Includes abbreviated journal lists
Web
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Sync
Creates exact copies (last
database updated will
update the other)
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Accessible from anywhere (via Internet)
Comes with Desktop or as a free
standalone
Free version does not allow attachments
Limited in size
Does not include abbreviate journal titles
EndNote Program Updates
Every few months you should check for program updates to see if a patch
has been released for EndNote. To do this, open EndNote, from the top
menu bar, select Help EndNote Program Updates. Click Next on the
Update window. You will then see a message that either says updates are
available, asking you to install OR a message that says EndNote is current.
Customize EndNote to work specifically with UW-Madison databases
After installation you may customize to:
1. Enable Finding Full Text when available from UW-Madison databases (open url/authentication)
2. Import Journal Terms List (full titles and abbreviations) for your subject/field (i.e. Medicine, Bioscience)
How to Create an EndNote Library (*.enl)
An EndNote library is your database of references, including any file
attachments.
1. Open the EndNote program on your desktop
2. From the top menu bar select File New
3. Save it on your computer wherever you prefer.
When you create a new library, another folder will automatically be
created with the same name, but will be a data folder. You will see a .enl
file and a .data file. These need to stay together. Do not delete the data
folder or separate it from the .enl library.
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How to Organize Citations using Groups within Your EndNote Library
Organize your citations into categories by creating custom folders (called groups). EndNote comes with three
permanent groups that cannot be renamed or deleted (All References, Unfiled, and Trash). There are also temporary
groups that are created by EndNote as needed such as Copied References, Duplicate References, Imported
References, etc.
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From the top menu bar, click on Groups > Create Group (you can have 500 groups/library)
In the left column of your screen you will see a box called New Group. Rename this to whatever you want
(i.e. Drug Lit, Cancer, Biology 101)
You can delete or rename groups at any time.
How to manually add a reference (only if you have to!)
1. From the top menu bar, select References > New Reference
2. Select the appropriate Reference Type, such as Journal article, from the drop-down menu (important because
it determines the fields that will show in the citation)
3. Enter information in the appropriate fields
o Author: One name per line (hard return <Enter>), with a comma after the author’s last name and
before the first name or any initials
o Corporate names should be entered as they appear with a comma at the end of the name for correct
alphabetizing (e.g. American Medical Association,)
o When typing in the title of an item, do not use the hard return (Enter key). Instead let EndNote wrap
the text for you.
4. Close the record and you will be prompted to SAVE click YES
5. Your record will be in the All References group by default. You can drag it into any group you want. The
citation can be placed into multiple groups.
How to add a reference automatically from a PDF
If you have the PDF version of a journal article, EndNote may be able to find the citation information and create a
reference from the PDF. The journal must have the DOI included in the article for EndNote to be able to locate the
citation information. Many journals include the DOI, although several do not.
You may import a single PDF or a folder with several PDFs into EndNote and the reference will be created
automatically.
To import a single PDF:
1. Select File  ImportFile
2. In the Import File field, choose the PDF you wish to import
3. In the Import Option field, select PDF from the dropdown
menu
4. Click on Import
To import a folder with multiple PDFs:
1. Select File  ImportFolder
2. In the Import Folder field, choose the folder you wish to
import
3. In the Import Option filed, select PDF from the dropdown
menu
4. Click on Import
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How to add a citation from PubMed
1. Perform a search in PubMed
2. Select references or leave boxes blank (all will export). On the upper righthand side, click on Send To, select Citation Manager and then select the
number of citations you want to send. Make sure it is more than the total.
3. Click on Create File
4. A file and/or window will appear. Click on the file.
5. EndNote will be launched or if you have a library open the citation will be
added to the library
6. Citation(s) will be added to the Imported References group. Move them
into the group of your choice because they will be overwritten the next
time you import records, but will be added to the All References group.
How to add a citation from Web of Knowledge (as an example of
a direct export)
1. Conduct a search in WoK.
2. Select the records you want to put into EndNote
3. Click on
4. Citations will export directly into an EndNote library. If it does not open, you will be prompted to open a library.
How to make changes to imported records (only) in EndNote
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Highlight all records you want to make changes.
Click on Tools, Change/Move/Copy Fields
Select a field (for example: Name of Database)
Select an option and enter text
Search Select Databases from within EndNote
You can search some databases online from within EndNote if the
database is open to the public or if is available through the UW. Note
some UW databases cannot be searched due to license agreements.
Example search using PubMed:
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Select the Online Search Mode (Temporary Library) icon
(upper left-hand corner)
Select a database or online catalog
Highlight the citations/references you want to save into EndNote
Copy the references by clicking References  Copy to 
choose the correct library
Go back to the Local Library Mode, select the Copied References
folder and move the references to a group of your choice
How to Add Individual File Attachments
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Mouse-click on the file (word, jpg, png, pdf, etc) you want to attach to an EndNote record and drag to the
proper record in EndNote and release the mouse-click
OR
1. Highlight the article you want to attach a file to
2. Right mouse-click to open menu, select File AttachmentsAttach File… (browse to a file)
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How to Find Full-Text Attachments Several Records at a Time
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Highlight the EndNote records that you want to find full text
From the menu at the top select References  Find Full Text  Find Full Text…
A UW-Library authenticate screen will pop up. Click on Continue
A Copyright Warning will pop up. Click on OK
On the left-hand panel, you will see the Find Full Text search results. If you selected several, it may take a
few minutes to populate. In general you can expect to obtain ~50%-60% of the items. Please note that this
feature will NOT pick up all the full text available via UW.
EndNote Cite While You Write (CWYW)
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Use the EndNote Cite While You Write (CWYW) Plug-in to insert references, and format citations and
bibliographies automatically while you write your papers in Microsoft Word.
EndNote CWYW software plug-in is automatically loaded into Microsoft Word when you install EndNote on
your computer. Please note that if you are an EndNote Web only (standalone) user, you will have to install
CWYW on your computer from the EndNote Web website.
Inserting References in your MS Word document
1. With your Microsoft Word document open, place the cursor in the location precisely where the citation should
appear.
2. Select the desired reference in EndNote and click on the insert icon
3. You can insert multiple references in one citation by clicking each reference while holding the Ctrl key.
1. From Microsoft Word, click on the Insert Citation icon
2. Click Insert
and search for the proper citation.
1. Highlight the reference in EndNote
2. Drag the reference to the correct location within Word
You can change the Citation Styles by using the Microsoft Word Drop-Down. If you don’t see the style you want,
select Select Another Style…. Once a style is selected, it will be retained in your drop-down menu.
Creating a quick bibliography in Microsoft Word
1. In an EndNote Library, select the citation style you want in the style drop down box (Annotated includes
abstracts)
2. Click on the records you wish to include in your bibliography (use Ctrl or Shift for multiple records)
3. Right mouse-click (or select Edit from the top menu) and select Copy Formatted.
4. Use the Paste options in Microsoft Word
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EndNote X6:
Transferring EndNote
Records
University of Wisconsin-Madison | 608.262.2020
http://ebling.library.wisc.edu | askebling@library.wisc.edu
Transferring Records between EndNote Desktop and EndNote Web
In EndNote Desktop
Moving records and attachments between EndNote Desktop and EndNote Web
 In EndNote Desktop you will see an ICON (blue button with two white arrows) near the top center of the
screen click on this to sync your library. Everything in both libraries will be synced in both directions.
Preferences for Syncing
You should only sync your EndNote Web to one EndNote Desktop Library!
In EndNote Desktop click on Edit/Preferences/Sync
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Here you can enter your email address and password for permanent storage
At the bottom of this screen you have three options for syncing frequency.
When syncing the EndNote Desktop library to the EndNote Web library ALL citations, figures, pdfs and
any other documents you have saved to records are saved to both libraries.
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Exporting/Importing EndNote Records (only) to/from EndNote Libraries
Export
1. Click on the records you wish to export (use Ctrl or Shift for multiple records)
2. Select File, Export… and create a file name. Save as a text file and select EndNote Export as the Output
style. Check the Export Selected References box if you wish to export only the ones selected.
Import
3. In a different EndNote library, select File, Import, File…
4. Find the <endnote>.txt file you wish import. Set the Import Option drop-down to EndNote Import and click
Import. The records (but not the attachments) will appear.
Exporting/Importing Entire Libraries
Export
1. Click on File, Compressed Library (.enlx)…
2. Select appropriate options on pop up box and click
Next
3. A compressed file <libraryname>.enlx will be
created. This file can be sent to others.
Import
4. Click on the <libraryname>.enlx file. It will open a
new library with the file name (same as the old
library name). All records and attachments will be
included.
Moving to other libraries on your computer
5. Select/highlight some or all of the references in one library
6. Select References on the top menu bar (or right mouse-click for quick menu)
7. Select Copy References To (choose or create a new library)
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EndNote X6:
Importing Terms List
(Journal Abbreviations)
University of Wisconsin-Madison | 608.262.2020
http://ebling.library.wisc.edu | askebling@library.wisc.edu
For accuracy in your bibliographies it is highly recommended that you download Term Lists (Journal
Abbreviations). Repeat the process for each library you create.
Note: if you have imported citations/references into your library before importing the Journal Term Lists
you must delete the Term Lists that were automatically created by the import process. To delete Term
Lists open your EndNote Library, go to Tools > Open Term Lists > Journals Term List. Hiighlight the
whole list and then click on Delete Term.
To import official Term Lists by subject area.
1. Open an EndNote Library.
2. Click on Tools > Define Term Lists.
3. Click on Lists tab > Journals > Import List.
4. Browse to find the folder named Terms Lists within the EndNote program which usually resides
at
c:\program files\endnote X6\terms lists\*.* on PC’s.
5. Click on the desired list from the following options and click Open.
+
6. The list will be imported into your EndNote library. Click on Tools > Open Term Lists > Journals
Terms List > Terms to confirm that you have now have at least one abbreviation list in addition to the
full journal title.
Note: Check your Output Style to verify whether a journal abbreviation or full journal title is selected.
Unless specified, the journal title will format as entered in the EndNote reference
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EndNote X6:
Enable Full Text
University of Wisconsin-Madison | 608.262.2020
http://ebling.library.wisc.edu | askebling@library.wisc.edu
How to enable the Find Full Text option to automatically import PDFs
From the Edit menu, select Preferences….
Select Find Full Text in the left-hand side window
Check all four full text search options
 In the OpenURL Path box enter: http://sfx.wisconsin.edu/wisc
 In the Authenticate with box enter: http://ezproxy.library.wisc.edu/login?url=http://www.library.wisc.edu
 Click Apply to save the setting
 Leave EndNote Preferences open for the next step
How to enable
in individual references
Next, select URLs & Links in
the left-hand side window
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In the OpenURL
Arguments box replace
=ISI:WOK with
=ISI:endnote
Click Apply to save the
settings
Click OK close the
preferences window
You are now set to use the
Find Full Text feature and
have an active Find It
button in each reference.
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EndNote X6:
Use Full Text
University of Wisconsin-Madison | 608.262.2020
http://ebling.library.wisc.edu | askebling@library.wisc.edu
**Follow the instructions on the other side before performing these steps**
To automatically find and import the full text (PDF) for references in your EndNote library:
 Highlight the reference(s) for which you want to
find PDFs
 From the References menu, select Find Full
Text…
 An authentication window will appear. Click
Continue.
 A copyright and usage notice will appear. Click
OK.
 EndNote will search the UW Madison licensed
resources for available full text PDFs. Paperclips will
appear in the reference citations for which full text PDFs are
found. A tally of the program’s progress will be visible in the
left hand sidebar under Find Full Text.
To access the
button:
Select a reference in the Library
window or open the reference.
 From the References menu,
select URLOpenURL Link.
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A
menu will
appear with options for accessing
full-text of that article.
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EndNote X6:
Install additional output styles
University of Wisconsin-Madison | 608.262.2020
http://ebling.library.wisc.edu | askebling@library.wisc.edu
The default EndNote installation includes only the 100 most popular output styles. However, there are over
3,700 different styles available. Journal styles are organized by discipline. You may download individual
styles from the EndNote website or you may install sets of styles by discipline.
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To install a set by discipline, close the EndNote program. You will need to start the installation
program as you would for a new installation.
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On your Windows PC, open the Control Panel.
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For Windows XP, select Add or Remove; for Windows Vista/Windows 7, select Programs and
Features.
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In the list of programs, highlight EndNote X6 and select the Change option.
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Select Modify, click Next.
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On the Select Features dialog window, click the + sign next to Additional Styles and select the
set you would like to install.
For each set of styles you would like to install, click the dropdown arrow and select either “Will be
installed on local hard drive” or “Entire feature will be installed on local hard drive”.
Click Next to continue with installation.
The styles will be copied to the EndNote styles folder and will be available for use the next time you
start EndNote.
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