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EndNote 8: FAQs

A Guide for Toronto Public Health Staff

Practice Using EndNote

If I want to practice using EndNote can I use a generic EndNote Library?

If you have EndNote installed on the computer you are currently using, you can access a Sample EndNote Library by:

1. Navigating to C drive > Users > Public> Public Documents > EndNote > Examples

2. Select and open the following file: Sample_Library_X8.enlx

Note: The ENLX indicates that the file is a compressed EndNote Library. The ENLX (compressed) Sample Library can be reopened multiple times. It will remain unchanged.  Opening this ENLX file will create the ENL file and Data folder with the same file name.   

You can practice and explore the functions and features of EndNote.  You can modifying this EndNote library (ENL file) in any way you wish (i.e. delete records, form groups, add citations, export citations etc.).  When you are finished practicing in the sample library, you can simply close the library.   


I don't have an online EndNote account. How do I share my Library with others?

Steps for creating a compressed EndNote Library (for sharing or for backup purposes):

EndNote uses the same name for the backup library as the original library, but adds a ".enlx" extension to show this is a compressed, or zipped, file. To created a compressed file:

1. Open the original library in EndNote (.enl file).

2. From the File menu, select Compressed Library (.enlx) to display a Compressed Library dialog.

3. Use the radio buttons to determine these options:

  •  Select (1) Create a compressed library or (2) Create & Email the library.
  •  Specify whether or not you want to save file attachments with the library (e.g. PDFs). Note: Be aware of copyright and license restrictions on PDF sharing. Do not save file attachments if you're sharing the EndNote library with external staff/unaffiliated staff.
  • Specify whether you want to save all references to the compressed library, only the selected (highlighted) references, or only the references in a specific group or group set.
  • Click OK Next to display a file dialog.

4. EndNote uses the same name for the backup library as the original library, but adds a ".enlx" extension to show this is a compressed, or zipped, file. Save the compressed library to a folder on your hard drive.


The easiest way to share a library is to compress your EndNote Library.  You can email an enlx file to your colleague if you're sharing contents.

How NOT to share a library:

  • Saving on USB

  • Saving on cloud services (i.e. Dropbox, Google Drive, Sharepoint, SkyDrive SugarSync).

Note: The way Cloud file storage services (i.e DropBox, Google Drive, Sharepoint, SkyDrive, Sugar Sync) sync files over the internet causes files to become corrupt over time.

Data in EndNote Libraries must be saved in a set sequence. When USBs or cloud services transfer data, they change the sequence of file saves to make the process faster.  This leads to EndNote Library corruption.

This video demonstrates library sharing: Library Sharing in EndNote X8 [Video, 04:15]


Saving your work in EndNote

How do I save my work in EndNote (I made groups, sorted items and deleted some records)?

In EndNote you do not need to save before closing the EndNote Library. All changes are automatically saved. (This is an adjustment for most TPH staff who are familiar with using Microsoft Word, where they may be saving their changes before closing a document.)


If you are saving two versions of a library, then you may want to name the Library with two distinct names. For example, staff 1 screening and staff 2 screening could be in two different libraries:

1. Rapid Review 2018_staff 1 screening

2.   Rapid Review 2018_staff 1 screening

You could drag and drop items from one library to another so that you can compare the screening decisions of your team members.

Journal Names & Abbreviations

How do I ensure Journal names appear consistently in my bibliography?

When you generate a bibliography or reference list you may notice that sometimes journal names are abbreviated.  In APA style you want the full Journal name rather than an abbreviated Journal name. If you need to create a reference list with consistency in Journal names, you can apply EndNote's Terms Lists.

Watch this video: 

What are PDF Auto Import Folders?


You can archive the PDFs you already have in an EndNote Library by using an Auto Import Folder.

What are Auto Import Folders?

You can designate a folder on your desktop as an "auto import folder." 

Simply save (or drag and drop) all your PDFs into this folder.

If the PDFs have a DOI (digital object identifier) Endnote will match this data in PubMed or CrossRef. If a DOI is matched on these sites, then you will have a record created with a PDF attached.

If EndNote can't find a DOI, it will create a record of the article in your library but there will be no PDF file attached. You can upload the PDF to this record manually.

Setup Process for PDF Auto Import Folders:

1. Create an empty folder on your computer and give it a name (e.g. PDF Auto Import for EndNote).

2. Open EndNote

3. Select Edit > Preferences > PDF Handling > PDF Auto Import folder

4. Navigate to the locations of the PDF folder

Whenever you open EndNote it will try to locate this folder and import the full text articles into your EndNote Library.

If you have 1 EndNote library for all your work projects, you can drag and drop PDFs into the same folder.

If you have discreet libraries for each project, you can have multiple PDF folders each with a distinct name.  Simply, set up your preferences in each EndNote Library to auto import PDFs from the appropriate PDF folder on your computer.  

Creating Groups: Custom Groups

How do I keep my Groups organized when I sync to EndNote Online?

EndNote online only syncs Custom Groups.  It does not track the Group Sets. You may have 5 group sets in your EndNote Desktop Library: CDC, CDIP, CHD, HC, HE 

When you sync to EndNote online (version 8 or version 9) these 5 groups will not appear. Only the Groups within the group sets will appear.

If you want all your contents to be organized, you can use prefixes in your Custom Group names and use consistent naming conventions so that when you sync to EndNote Online, all your Groups will remain organized. Example:    

CDC: influenza MEDLINE 2017

CDC: influenza MEDLINE 2018

CDC: vaccine hesitancy MEDLINE 2018   

CDIP: concussion prevention MEDLINE 2010

CHD: breastfeeding and cannabis MEDLINE 2018

CHD: speech and language MEDLINE 2018

HC: community violence MEDLINE 2018   

HE: bedbugs MEDLINE 2018

HE: eCigarettes MEDLINE 2017


Formatting References in APA Style

When writing a report or preparing a presentation you may need to reference the items you gathered in your Endnote Library.  In order to format your references appropriately, you can refer to the following resources:

To find APA formatting rules refer to:

  1. APA Style Guide (by OWL Purdue University)

  2. APA videos (by OWL Purdue University)

  3. Publication Manual of the American Psychological Association. (Call # BF 76.7 P83 2009 – reference section of TPH library)

  4. Concise rules of APA Style (Call # BF 76.7 P8 2009 – reference section of TPH library)

To use EndNote to cite while you write your report use the following guides:

  1. Cite While You Write: Formatting your Bibliography (by Clarivate Analytics)

  2. Formatting your bibliography in MS Word (by University of Canterbury)

I need more help with EndNote

Creating Groups: Smart or Combination Groups

How do I create specialized groups within my EndNote Library?

In EndNote you can tag your results with a Group label (these appear as items in a folder).  Items in EndNote can fall in multiple groups.

There is no limit on the number of Groups you can create.

Keeping track of results in properly labeled groups will help you complete your PRISMA flow diagram.

In EndNote there are three types of Groups:

Group Type Icon Use Example
Custom Groups

pages/ documents

Custom Groups are used to identify a set of references.

If you export results from PubMed or CINAHL you can place the PubMed items in one Custom group and the CINAHL results in another Custom Group.



From (combination) Groups

Venn diagram/ overlapping circles

From Groups are used to combine Custom Groups

If you want to compare, combine or review all search results from multiple groups you can form a "From Group".

Scenario 1: Use "OR" to gather results from multiple groups (e.g. combine results from all databases by using MEDLINE OR CINAHL OR SocIndex OR Cochrane DSR).

Scenario 2: Use "AND" to compare results appearing in separate groups (e.g. to find duplicates in "Minakshi's Included Records" AND "My included Records"). The records you find show that you're in agreement with your partner about these records and you can retrieve full text for screening or critical appraisal purposes. 

Scenario 3: Use "NOT" to find what is unique to one group (e.g. "My included records" NOT "Partner's included records" will show you items that you included but your Partner did not include.  Use this strategy to identify records and reach concensus about included studies).

Smart Groups

gear or cogwheel

Smart Groups are used to identify items that meet specific search criteria.  For instance, you can locate articles with the phrase "public health" in the title. You can form a "Smart Group" by searching the phrase "public health" in the Title field to identify all items in your library which meet this search criteria.