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Choosing a Citation Manager: From Endnote

This guide will outline how to switch to a new citation manager like Endnote, Zotero, or Mendeley

Created by Health Science Librarians


Endnote is designed to be a research manager like Mendeley which handles primarily PDFs. There are some drawbacks to Endnote, which may cause some users to want to switch to another citation manager, like perhaps Mendeley or Zotero.

On this page, we will outline the steps that you need to go through in order to transfer your Endnote library to another citation manager.

Exporting your citations from Endnote

To export your citations from Endnote, you need to follow these steps. But also keep in mind different citation managers prefer different output formats from Endnote. Consult this table to see which you should choose:

New Citation Manager Output format
Zotero XML
Mendeley XML
  1. Open Endnote
  2. Click on the Export option in Endnote. Like so:
    Clicking File then Export to save a copy of your Endnote Library to import into Zotero or Mendeley
  3. Now for the next window, the output style section is not important. But you do need to be sure to select the XML type under the Save as type section. Like so:
    Selecting the XML file type when you export your Endnote Library

Now you have your references ready to import into the new citation manager!

Importing your citations into Sciwheel (F1000)

1. Log in to your Sciwheel (F1000) account and navigate to My References

2. Select the Import References button.

3. From the resulting menu, drop down References to view your options.

4. Select the icon of a page with an asterisk labeled RIS, BIB, NBIB & EndNote XML files.

5. Select the file that you exported from EndNote and click open.

Importing your citations into Zotero

  1. Open Zotero and click on the Gear icon and select Import. Like so:
    Selecting the Gear Icon then Import to import references from Endnote into Zotero
  2. Select the file that you exported from Endnote and click open

Importing your citations into Mendeley

  1. Open Mendeley and select File then Import then Endnote XML - Endnote x8, X1 to X3 (*xml). Like so:
    Selecting File then Import then File in Endnote to import citations from Mendeley
  2. Choose the file that that you exported from Endnote and then click on Open.