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EndNote: Adding References fom PubMed database

How to use EndNote software to save, manage, and print citation information within your papers.

Import from PubMed Database Searches into EndNote

NOTE: to set up alerts please check out my Creating Publication Alerts LibGuide.

No database indexes every publication.  We strongly suggest that you search every database in this section of the LibGuide to compile the most complete EndNote libraries.

You can search and retrieve references from PubMed in two ways

  • directly from PubMed database
  • from within an EndNote Library
NOTE: The directions in this page are exactly the same for both Microsoft and Mac OS
NOTE: Directions for eliminating duplicates, deleting and recovering references are at the bottom of this page

From PubMed to directly to  an EndNote library

To upload references directly from PubMed.

1.   Open the EndNote Library into which you want to import references (e.g. Wigler Publications).

2.    Access PubMed database from the Library web site.
Note: Accessing PubMed from the Library web site automatically accesses all our subscription journals for retrieving publications.
3.    On PubMed home page select the Advanced search option and perform a search.


4.    In the Search Results window

  • click the references you want to export.
  • Click on Send To
  • In the drop down window click on File
  • Under Format choose MEDLINE
  • Click Create File

5.    Click Save in the popup window

6.    Save the text file (labeled pubmed_result) to your desktop, or you can create a PubMed results folder.

Now that you have created a text file of PubMed search results you can upload the file into your EndNote Library.

7.    Click on File

8.    From the dropdown click on Import then File.

9.    In the Import File window;

  • select the pubmed_result text file you just created and click Choose
  • For Import Options select PubMed (NLM) in the dropdown list
  • If PubMed is not listed, select PubMed from Select Filters dropdown list
  • Click on Import

Your records will be uploaded into your EndNote Library

How to search and retrieve PubMed references from within EndNote

1     In an open Library, click on Tools, Online Search,

2     From the Connection Files list choose PubMed (NLM). Click Choose,

The database should appear under Online Search in My Groups

Shortcut: You can also also add connection files by clicking on more under Online Search


3.    Go to search and upload references directly from PubMed above and do steps 3 to 9

Eliminating duplicates from your library;

  • Click on References in the top tab
  • Click on Find Duplicates
  • Review and select which one of each duplicate you want to eliminate

Removing references from your library;

  • highlight the references you want to eliminate
  • Click on References in the top tab
  • Click on Move References to Trash

To move references from trash back into your library

  • Click on  the reference(s) in the trash group you want to restore
  • Click on References in the top tab
  • Click on Restore to Library

Subject Guide

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Tom A
Cold Spring Harbor Laboratory
One Bungtown Road
Cold Spring Harbor, NY 11724

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