EndNote Manuals


Download custom EndNote Filters and Styles

To install a custom filter of style: open the zip file, double click on the desired filter or style. In EndNote click on File > Save as. This zip file contains the filter that are mentioned in the descriptions below.

In general it is recommended to use the specially created import filters marked with "label". These will copy the pmid into the field label, which allows you to deduplicate on PMID via the field label.

I have developed a series of videos on the deduplication method that are available through Youtube:
Phase 1: Change Settings
Phase 2: Normalize Imported References
Phase 3: Selecting and Removing Duplicates

Steps in the deduplication process:

  1. Go to Edit > Preferences > Duplicates
  2. Fill in the fields of the first column in the list to Compare Duplicates and click [OK]
  3. Go to All References and click on one random reference to activate this list
  4. Go to Library > Find Duplicates
  5. In the next screen click [Cancel] (watch out, not in step a)
  6. Follow the instructions in the second column of the table below
Set Field Preferences (step 1)Steps to remove duplicates (step 6)
aLabelIn step 5 (see above), first click Skip, then click Cancel. Next press [Delete] to remove all selected duplicates without manual assessment
bAuthor | Year | Title | Secondary Title (Journal)Press [Delete] to remove all selected duplicates without manual assessment
cAuthor | Year | Title | Pages
dTitle | Volume | Pages
  1. Manually assess the top references with blank title or author fields, using [Ctrl-Click] to deselect false duplicates.
  2. Click on the column heading 'Pages' to sort all duplicate references by ascending order of page numbers.
  3. Deselect the top references without page numbers by pressing [Ctrl-click] on the first highlighted reference, and [Ctrl-Shift-click] on the first highlighted reference with a starting page number greater than 1. Remove the remaining selected duplicates with [Delete].
eAuthor Volume Pages
fTitleCompare page numbers of consecutive references. If page numbers are present and different, examine journal titles and authors. Deselect false duplicates with [Ctrl-Click]. Blank pages or pages starting with the number 1 are usually true duplicates, but check journal titles and author names when in doubt, especially when multiple consecutive blank pages are selected. After checking the entire list, remove the remaining selected duplicate references with [Delete].
gAuthor | YearIf a true duplicate is found, deselect all references by clicking the first true duplicate reference without holding [Ctrl]. Compare subsequent references on page numbers: if two adjacent references have the same page numbers, select the one with the largest record number with [Ctrl-Click]. After checking the complete list, remove the remaining selected references with [Delete].

To ease the deduplication process in EndNote it is recommended that instead of using the traditional export and import workflows you use the following steps.


We recommend you either search PubMed or Medline via Ovid, there is no need to search them both
  1. Export References via Send to > Citation Manager
  2. You can directly open the file to import into EndNote

Medline via Ovid

We recommend you either search Medline via Ovid or PubMed, there is no need to search them both
  1. Export References via the link Export
  2. Select the Format 'Reprint/Medlars', and the Fields 'Complete Reference'
  3. Save the .txt file locally
  4. In EndNote go to File > Import > File
  5. Select the .txt file and use the Import Option _Medline Ovid Erasmus MC

Correction of Page Numbers for Medline and PubMed

Page numbers in PubMed and Medline are exported abbrevated. This mean an article ranging from age 1008 to pag 1012 will recieve a page number in EndNote that reads 1008-12. This needs to be corrected.
  1. Select all references that you have imported from PubMed or Medline Ovid bij going to 'All References' and clicking Ctrl-A.
  2. Go to File > Export
  3. Select the Output Style '_Correct Pages'
  4. Save the output locally as a text file
  5. Close the EndNote library you were working in
  6. Go to File > New and create a new EndNote Library with the same name as you had before and overwrite the old library
  7. Now import the references from PubMed or Medline Ovid:
    1. Go to File > Import > File
    2. Select the .txt file that was created above and use the Import Option '_Import Corrected Pages'
  8. It is wise to gather references from each database together in a group:
    1. Right click on 'My groups'
    2. Type the name of the database for the name of the group
    3. Go to imported references, select all references (Ctrl-A) and drag them to the new group


We don't have access to Embase via Ovid. Therefore we cannot recommend on how to export those references
  1. Select the total number of references with the option 'Select number of items'.
  2. In the Results menu click on 'Export'
  3. Select the RIS format (standard selection) and click Export
  4. In the new tab download the file .ris and save it locally
  5. In EndNote go to File > Import > File
  6. Select the .ris file and use the Import Option embase Erasmus MC