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EndNote, RefWorks and Other Citation/Reference Managers

Tips on choosing and using citation/reference/bibliographic management software including EndNote, RefWorks, Zotero and Mendeley.

Choosing citation/reference management software: which one is right for me?

These key points refer to EndNote, RefWorks, Zotero and Mendeley:

  • If you don’t want to pay for software, consider RefWorks (UCSF only), Zotero, or Mendeley.
  • If you want open source software, choose Zotero.
  • If you want software that's easy to learn, choose RefWorks (UCSF only).
  • If you want to mainly work offline on your own computer, consider EndNote or Mendeley. You can do this with  RefWorks but it takes a bit more effort.
  • If you want easy online access to your references, consider RefWorks. EndNote Web/Online and Mendeley also permit this, but with fewer features than the desktop versions.
  • If you save a large proportion of the material you use as PDF files, Mendeley may offer significant advantages, particularly if you’re a scientist.
  • If you're writing a dissertation and want software that's powerful and can be customized to your specific needs, consider EndNote, though Zotero offers many of the same features and is free.
  • If you're interesting in using the software to collaborate with colleagues, consider using Zotero and Mendeley, though EndNote users can share references and PDFs using EndNote Online.  .
  • If you want to sync your library with multiple computers, choose Zotero or Mendeley.
  • If one system doesn’t meet all your needs, consider the possibility of integrating two or more.

This is an attempt to provide a brief overview of four popular citation management software. The key to choosing the right software depends on deciding what you want to use it for!

More information on EndNote, RefWorks, Zotero and Mendeley.

Comparison chart for all currently available managers

Comparison table for EndNote vs. RefWorks

EndNote and RefWorks are the two most popular managers here at UCSF, so this table compares features for just these two.




Access Endnote must be installed on your computer. However, users have access to EndNote Web, a stripped down online version of EndNote. Web-based, making it fully "portable." You install the Write-n-Cite plugin to create bibliographies with MS Word. If you wish you can also download your references to a computer and work offline.                                  
Ease of Use More fully-featured than RefWorks so slightly more difficult to use. Simpler than EndNote and easier to learn.
Cost Individual must purchase own copy. Free to UCSF students, staff and faculty. Create an account here. After graduation, UCSF alumni can retain account.

Format Bibliography in Word

Yes, via Cite-While-you-Write plugin.


Yes, via Write-n-Cite plugin.



Windows/Mac Different programs for Mac & Windows.

Same for both Mac and Windows, though there are different versions of the Write-n-Cite Word plugin


Links to UC-eLinks

Yes, but user must configure software.


Yes, automatically linked.

Automatically Retrieves Full-Text

Yes, with version X2 or higher. No

Store PDFs

Yes Yes

Ability to Annotate PDFs

Yes, with version X5 No

Create a Formatted List of Figures & Charts.

Yes No
Support for Mobile Devices

Version X2 and above includes application for Palm OS® handheld devices.


RefWorks Mobile for mobile & smart phones
Support for iPAD Search PubMed using EndNote Web.

You can access RefWorks with Safari on your iPad and import, edit, and organize references as you normally would.



Limited, using a Travelling Library and EndNote Basic (aka Web)


Share database (or folders) with members of own institution and globally with any researcher using RefShare.


More Information

EndNote FAQ

RefWorks FAQ

Comparison table for most popular applications

  EndNote Desktop EndNote Basic Mendeley RefWorks Zotero Papers
Cost Individual purchase by user, research group or department.

Free to everyone.

Basic application free to everyone. Free to UCSF faculty, student and staff. Basic application free to everyone. Individual purchase by user, research group or department.
Platform Mac, Windows Web-based, so indepenent of platform. Mac, Windows. Web-based, so independent of platform. Mac, windows Mac, windows  
Share references with  other citation management programs Yes Yes Yes Yes Yes Yes
Creates formatted bibliographies Yes Yes, MS Word only Yes    Yes Yes Yes
Link to PDFs or other materials Yes Yes Yes, including Web snapshots. Yes Yes, including Web snapshots. Yes
Retrieve PDF citation data Mixed results No Mixed results No Mixed results Mixed results
Add notes to references Yes Yes Yes Yes Yes Yes
Annotate PDFs Yes No Yes No No
Retrieve PDFs Yes No Yes No Yes Yes
Direct Search of Online Databases Yes Yes Automatic capture Yes Automatic capture Yes
Direct Export from databases Yes Yes, with specific databases Yes Yes Yes Yes
Store PDFs Yes Yes Yes Yes, but only available with institutional subscription. Yes Yes
Edit or create styles Yes No Yes Yes Yes Yes
Collaboration features Traveling Library within a word processor document
Syn with EndNote Basic
Share EndNote Web references with other EndNote Basic users.


Create public and private groups. Automatic synchronization of collections among multiple computers

Share references if institution has subscription to RefShare.


Create public and private groups. Automatic synchronization of collections among multiple computers

Mobile Device Application iPad, web interface No iPad, iPhone, web interface RefMobile for mobile and smart phones. 3rd party, web interface Yes
Capture web page content No No Yes No Yes No
RSS Feeds No No Yes Yes Yes No

Reference Management Software Overview PPT (2015)