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There is currently an issue with the EndNote filter when exporting citations from any Ovid database (MEDLINE, Embase, Emcare, APA PsycInfo, etc.). To avoid issues, please select the RIS format when exporting citations.

EndNote overview

EndNote 20 logoTo prepare for screening, we recommend you export your database search results into EndNote.

For stability and ease of use, we suggest you use EndNote Desktop rather than EndNote Web.

If you are new to the program, start by familiarising yourself with EndNote generally. The Library has a range of resources available to support you.

Step 1: Build your EndNote library

Organise your references
  • Create a new EndNote Library (File > New) to use solely for your review.
  • Create and name the group for each database/source you searched (See example image).
  • As you search each database, export all results from that database into the matching EndNote group. This will allow you to report the total references found in each.
Screenshot of EndNote Groups and Group Sets

If you plan to deduplicate using EndNote, export records from high quality sources first - as EndNote will send the most recently added records detected as duplicates to the 'Trash', retaining those added first. Databases on Ovid such as MEDLINE are a good place to start, followed by other reputable databases such as CINAHL. Add records from Web of Science and/or Scopus after the key databases with subject headings, and before incomplete/error-prone sources such as Google Scholar.

Exporting references from Ovid Emcare

When exporting from Ovid Emcare, you may be prompted to use an 'Import Filter'. Select the EMCARE (Ovid) filter. If this does not appear in your list, select 'Other Filters' and search for it. If the filter still does not appear, search for it in the EndNote Import Filters page, which lists new and updated filters to download.

To download and install a filter:

  1. Close EndNote
  2. In your browser, select the filter link
  3. Save the file in your filters folder:
    • Windows: C:\Program Files\EndNote #\Filters (Where # is the version number for EndNote)
      Mac OS: Applications\EndNote #\Filters (Where # is the version number for EndNote)
    • see Folder Locations for more information
  4. Open EndNote - the filter should now be listed

Learn more:

Step 2: Back up your EndNote library

It is a good habit to back up your EndNote library. Specifically:

  • keep at least two of the same back-ups in different locations,
  • back-up on a regular basis or;
  • whenever you make significant changes (e.g import from a database).
Create a back-up library
  1. Select File > Compressed Library (.enlx)
  2. Follow the prompts and name the file
    (e.g. my_review_backup_29_5_2020.enlx)

image example of a compress Endnote library


Note: .enlx is a zipped file that combines your EndNote library (.enl) and Data folder together, enabling you to restore the file easily.

Learn more:

Video Length: 2:15

Step 3 (optional): Deduplicate your EndNote library

Note: Skip this step if you are using Covidence for screening, as Covidence will perform its own deduplication.
Rename your group

Before you deduplicate your references in EndNote, rename your groups by adding the total number of results from each database (see example image), for reporting purposes. 

To rename a group:

  1. Right-click on the group
  2. Rename group
  3. Next to the database, add total number
    e.g. Cochrane Library (68)

The total number of references will need to be reported in your PRISMA flowchart.


Screenshot of renamed groups
Deduplicate your references

Use EndNote's Find Duplicates function to remove multiple copies of references. (X9: References > Find Duplicates; 20: Library > Find Duplicates).

This will change both:

  • the number of results displayed next to each group; and
  • the total number of references in your library.
Note: EndNote can miss duplicates! You should also manually check for them by re-sorting your library by title (select the Title column heading) and deleting any duplicates you see.

Learn more:

Video Length: 1:03

Step 4: Export your EndNote library

Now that your Library is complete, you can export the references within it to commence screening:

  • Select all All References (located above the Groups list).
  • In the Menus, select File > Export

An export window will appear (for simplicity, we suggest saving to the Desktop).

  • Untick "Export Selected References".
  • Make the following selections:
If you are screening in: Save As Type Output Style
Excel XML Tab Delimited
Covidence Text File (*.txt) RefMan (RIS) Export


Note: If you cannot see the required Output Style, choose 'Select Another Style' and then search for it. 

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