EndNote, RefWorks and Other Citation/Reference Managers

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

What is citation/reference management software & what can it do for me?

Citation management software (also known as reference or bibliography management software) is a tool that allows you to:

  • collect and keep track of journal articles, books and other resources
  • store references on your computer or in a web-based account
  • cite references and create bibliographies in word processing software
  • link to full text

Some have additional features that let you:

  • share your references
  • automatically download PDFs
  • annotate PDFs
  • collaborate
  • use it for professional social networking

Which one is right for you?

Below are some of the common questions you should consider before choosing:

  • is it free or do you need to pay a fee?
  • do you plan to use it to just produce a biblography for the occasional paper or do you intend making it a central tool for managing your information?
  • are you prepared to spend some time learning how to use it effectively?
  • does it support the journal styles that you will need?
  • are help and support readily available?
  • does it allow you to easily share references with others?
  • do you want to store PDFs?
  • do you want to use it on a mobile device?

Comparison table for EndNote vs. RefWorks




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