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This Is Auburn Auburn University Libraries LibGuides

EndNote: Useful stuff to know


EndNote is a great way to store PDFs.

Use groups to organize references by topic.


Links to content

Adding references to EndNote
       Manual entry
       Direct export => From a database (PsycINFO, Web of Science, etc.) 
       Two-step => From a database (PubMed and SciFinder) in two steps
       From EndNote => Search PubMed and the AU Library catalog from EndNote
       Via PDFs  => Drag & drop a PDF onto EndNote to create an EndNote record
Change case – For article titles
Duplicates – Avoiding (and removing)
Editing references
EndNote Web
Formatting references in Word
Formatting the layout of references in Word
Full-text – Finding and downloading
Groups – Organizing references into folders
Import filters
Journal abbreviations
Output styles – Finding
Output styles – How to edit
PDFs – Storing in EndNote
PDFs – Viewing and quick editing
Reference list – Creating a list to review
Reference list with abstracts 
Searching an EndNote library
Writing papers in Word -- And some tips worth checking out

Change case -- In article titles

If there are words in article titles that must be capitalized a certain way, then Preferences can help.

Edit --> Preferences --> Change Case --> Add the term whose case should not change (e.g., geographical names, gene names, acronyms, and irregularly capitalized words such as EndNote).

Duplicates -- Avoiding (and removing)

Avoiding duplicates

It is best to not have duplicates of a reference in an EndNote library. This can become problematic, especially if different versions of the same reference are cited in a Word document. To avoid this, edit the preferences.

Edit --> Preferences --> Duplicates --> Check the box for Automatically discard duplicates

Removing duplicates

It is best to avoid adding duplicates in the first place (see above), but if you already have …

From the References menu, select Find Duplicates. This allows you to find and remove duplicate records.

Editing references

In the EndNote record 

Although Word allows one to make changes in the citations within the "gray text" of the cited references section, do not do this! If you ever reformat the "changed" Word document, any changes made within "gray text" will be undone when Word looks back at the EndNote library for details about the citation. Instead, make the changes to the citation in the citation record in the EndNote library.

For author-date styles, edit in the citation in Word

If you are using an Output Style that uses parenthetical author / year in the text of the Word document (Smith, 2000), you can edit a specific citation to make changes such as adding page numbers or suppressing the author or year. Place your cursor on the reference in the text. On the EndNote ribbon, click on Edit & Manage Citation(s) and edit the citation as is needed. This will only change how that particular citation looks -- no other citations are affected. If a page number(s) needs to be included, try the Pages box. If that does not work, then use the Add suffix box to insert page numbers.

EndNote Web

Two years of access to EndNote Web comes with a purchase of EndNote. EndNote Web is a cloud computing version of EndNote. It can be a convenient place to keep your EndNote libraries as you move between different computers. You can move references from EndNote into EndNote Web and vice versa. Almost everything that can be done with EndNote can also be done with Endnote Web. However, most things are done slightly differently in EndNote Web than in EndNote. Learn how to use EndNote first. Then learn how to do the same thing in EndNote Web. There are good tutorials in EndNote Web. If you decide to rely on EndNote Web, it is recommended that you upgrade every time a new version of EndNote is released. This should keep your access to EndNote Web active.

Auburn University students, staff, and faculty have free access to EndNote Basic. This is not the same as EndNote Web. One difference is that the free version EndNote Basic limits the number of references to 10,000. A more significant difference is that EndNote Basic does not allow PDFs to be attached to the records.

Formatting references in Word

EndNote can format a paper in over 5,000 citation styles. Simply choose the desired style format or specific journal (e.g., MLA, APA, Int. J. Cancer, etc.). EndNote calls these "output styles". The same Word document can be quickly and easily formatted in different output styles.

  1. Open the EndNote library used to write the Word document.
  2. Open the Word document.
  3. Click on the EndNote ribbon click on the downward arrow next to Styles (middle of the ribbon).
  4. Click on the style you want. This instantly reformats the paper int the new style.
  5. If the style you want is not listed, choose Select another style and find the style you want to use. As soon as you click on the new style, the paper will be reformatted in the new style. If the style you need is not lised in Select another style, go to Downloads at to download the latest Styles. If the style you need is stillnot there, the best thing to do is to find a style that is close to what you need and then to edit that style to meet the style required by the journal (see Output Styles -- How to edit).

Formatting the layout of references in Word

You may not like how EndNote references are formatted by Microsoft Word. To change the font, font size, or the line spacing in the Reference section, click on Edit & Manage Citations (on the EndNote ribbon in Word).

--> Edit Citation --> Tools (lower left of the box) --> Configure Bibliography --> Layout tab

Full-text -- Finding and downloading


Select references --> Click on the Find Full Text icon (top of page)


Select references --> Choose Find Full Text from the References pull-down menu --> Find Full Text ...


EndNote X8 can find and download PDFs into EndNote. This works for many, but not all, PDFs to which Auburn University has access. When it works, it is probably the best way to add PDFs to EndNote records. The reasons why Find Full Text may fail are: 

  • The DOI is not included in the reference. Some databases do not include an article's DOI when they index the article. 
  • Some publishers are not accessible by Find Full Text. For example, JAVMA published by the American Veterinary Medical Association do not currently work with Find Full Text (this may change). 
  • Off-campus access to journals can be problematic due to authentication issues. There are two ways to handle authentication when not on campus.
    • Use VPN when working off-campus -- this allows you to work as if you are on campus.
    • Edit --> Preferences --> Find Full Text --> Make sure the OpenURL box is check and in the OpenURL Path box enter

Getting started

To start a new EndNote library ...

Open EndNote --> File --> New --> Name the new library (aka file) and Save it to a convenient location.

This creates a file and a folder with the same name. Both are important. The folder contains all of the PDFs that have been stored in an EndNote library and a few more details about the file. The file contains all the information about the references. To back up an EndNote library make sure to back up both the file and the folder.

Important: If you might publish in journals that use journal title abbreviations, then create a Journal Term List now!

Groups -- Organizing references into folders


Groups are simply folders in an EndNote library into which references may be placed. The same reference can be placed into more than one group. Group Sets are folders that can contain other folders, which offers more ways to organize references. Smart Groups automatically add references to the "Smart" group, but only if they match search criteria -- both from references currently in EndNote and from those added later.


EndNote X3 to X9 => Right click on a Group Set --> Create Group --> Name --> Enter
EndNote X1 & X2 => Right click on the left column --> Create Group --> Name --> Enter

Group Sets

From the Groups pull-down menu --> Create Group Set --> Name --> Enter

Smart Groups

Right click on a Group --> Create Smart Group --> Set search criteria --> Name --> Enter

Import filters

What is an import filter?

An import filter is like a traffic cop. It directs parts of a reference (e.g., journal name, volume, pages) from a database into the correct place in an EndNote record. If EndNote is not importing references correctly from a database, you may need to download a newer version of the import filter. To make it easy to find the right import filter for databases used at Auburn University, go to Filters for AU. Save the import filter to c:\program files\EndNote\filters.


Two common import filter problems 

  • EndNote cannot find the import filter that you need. Starting with EndNote X3, only the “top 100” import filters are included. EndNote does this so that it works faster with Word. Many of the import filters needed for the databases provided by Auburn University Libraries are not in the “top 100”.
  • Parts of the reference (journal name, author, article title, volume, page numbers) are not being placed in the right place in the EndNote record. 

There is probably a newer import filter that will work better. This can happen through no fault of EndNote. If the database (e.g. MEDLINE, Agricola) or the vendor (e.g., Ebsco, Ovid, NLM) changes how information is organized in their records, then EndNote import filter needs updating. The solution for both problems is the same: Go to EndNote and get the latest import filter for the database and vendor.


How to get the latest import filter 

Auburn University students, faculty, and staff can download the newest import filters via the Filters for AU tab in the EndNote guide This tab has links to the most recent import filters for the databases to which Auburn University subscribes. 

If the database you need is not listed on the Filters for AU tab, then first determine who the vendor for the database is. You will need to find and download the import filter for the database AND the correct vendor. The major vendors for Auburn University databases are Ebsco, OVID, and ProQuest. Go to the EndNote homepage. Under Downloads, select Filters. Find the import filter for the database AND vendor combination that you need and download the file. Save the file to c:/program files/EndNote/filters.

PDFs -- Storing in EndNote

There are four ways to get PDFs into EndNote.

• Right click on an EndNote reference --> File Attachments --> Attach file … --> Browse to the desired PDF and click Open
• See Full text – Finding and downloading
• See Adding references to EndNote – Via a “PDF folder”
• Drag a PDF onto an EndNote record.

A paperclip will appear in the far left column in EndNote if a file if attached to the record. Most of the time, the file is a PDF of the paper. This makes it easy to tell at a glance in EndNote whether you have already downloaded a copy of the PDF.

IMPORTANT: EndNote creates a copy of the PDF and stores in a file that has the same name as your EndNote library. EndNote inserts a link to the PDF in the record which links to this saved file. If you make a copy of the EndNote library, then you should also make a copy of the folder that bears the same name. Both files are necessary for EndNote to function properly.

PDFs -- Viewing and quick editing

  1. In EndNote, place the cursor on a reference to which a PDF has been attached. This selects the reference.
  2. Look for the PDF tab. This is usually on the bottom of the page but its location depends on which layout option(s) you have selected. [Aside:  The “left column” and “bottom split” layout is a nice option].
  3. In the PDF tab, you can highlight sections, insert notes, and search the PDF.

Reference lists -- Creating a list to review

    1. First choose an Output Style in EndNote. Edit --> Output Styles --> Select the desired Output Style by putting a check mark next to it. If that Output Style is not listed, then click on Browse ... to see other Output Styles.
    2. Return to the Edit menu and choose Select All to highlight all the references in a library (or in a folder). Alternatively, use the control key to select specific references.
    3. Return to the Edit menu and select Copy Formatted.
    4. Paste into a Word document. This inserts the references into Word in the Output Style selected in Step 1.

Note: For a quick printout from EndNote, follow steps 1-4 above, then click File in EndNote and select Print.

Reference list with abstracts

This is a nice format in which to summarize and review your references. EndNote comes with a generic output style called "Annotated"  which can be chosen as described in Step 1 above in Reference lists. However, any Output Style can be edited to display the abstract.

To edit an output style to include the abstract:

Edit --> Select Output Styles --> Edit "Your chosen output style" --> In the left column, choose Layout under Bibliography --> In the "End each reference with" box use the "Insert Fields" button to insert an End of paragraph, a second End of Paragraph, an Abstract, and a final End of Paragraph.

Then save the changes. It is that easy to edit an Output Style.


Searching an EndNote Library


  • Use the Quick Search to do a keyword search in your EndNote Library (screen top). This feature makes an EndNote library your own personal searchable database.

  • If you want to search specific fields (e.g., author, year, etc.), use the Search Panel (screen top). If it is not displaying, click on Show Search Panel (top right). 


Writing papers in Word -- And some tips worth checking out

Insert citations in a Word 2010 document

    1. Open a Word 2010 document and click on the EndNote ribbon at the top of the page.
    2. Place the cursor where you want to insert a citation(s).
    3. Go to your EndNote library and highlight the citation(s) you wish to insert (use CNTL for multiple citations).
    4. Return to Word 2010. Under the icon called Insert Citation (on the far left of the EndNote ribbon, page top) click on the little arrow and choose Insert Selected Citation(s).
    5. It may take little while for EndNote and Word to “talk”, but once they do, the citation(s) will appear in Word. After the two programs are “talking”, inserting citations is much faster.
    6. Don't worry if the citation style in the Word document is not what you want because that can be easily changed (see Output styles – How to edit).

Another way to insert citations in a Word 2010 document

    1. Open a Word 2010 document and an EndNote library.
    2. Place the cursor where you want to insert citations.
    3. Click on the EndNote ribbon at the top of the page.
    4. Under the icon called Insert Citation (on the far left) click on the little arrow and choose Find Citation ...
    5. Enter one, or more, keywords to search the EndNote library (e.g., year, author, article title word, etc.).
    6. Highlight the citation(s) that you want to insert. Click Insert.

Tips for getting references to look right in Word

How to handle superscripts, subscripts, italics and more in EndNote references

  • Edit the EndNote record (not the Word document) with the desired superscripts, subscripts, italics, bold, and underlining.
  • Remember that capitalization within article titles is handled by Change Case (see page 6 above).

Special characters, accents, and diacritical marks – An easy and a less easy way

  • Easy way => This works for most Greek symbols. In the article title field in the EndNote record click on the sigma (Σ) button and type “a”, “b” to introduce Greek symbols (e.g., α, β) in the article title. Use the Shift key for some capital Greek letters (e.g., Σ, Δ, Φ).
  • Less easy way => This works for everything. Copy the desired Special Character from the Windows Character Map (Start --> Programs --> Accessories --> System Tools --> Character Map) and paste it into the article title field in the EndNote record. You may need to change the font—for scientific symbols, use the Symbols font.        

Why doesn’t the formatting in my EndNote references match the rest of the Word document?

Word --> EndNote ribbon --> Bibliography --> Click on the little arrow (bottom right)

  • The Format Bibliography tab changes the Output Style.
  • The Layout tab controls font size, font style, font format, line spacing and line indentations.                    

How to handle superscripts, subscripts, and italics in EndNote references

  • Edit the EndNote record with the desired superscripts, subscripts, and italics. Remember that capitalization in article titles can be handled by Change Case (see page 6 above).
  • For example, Th4+, UO22+, and italicized ortho are handled in the EndNote record title field.