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EndNote, RefWorks and Other Reference Managers

Tips on choosing and using reference managemers (AKA citation managers) including EndNote, RefWorks, Zotero, and Mendeley.

What are they? What do they do?

In essence they all do the same three things:

1. Store information about books, articles, websites, etc. in one place.

2. Organize this information is a useful way and search to find what you seek.

3. Use the information in your reference manager to add in-text citations and a reference list to a document you are writing.

They vary in many details.

We will focus on 4 (EndNote, RefWorks, Zotero, F1000). There are many others available. As I write this in early 2019, the last year has seen 2 reference managers merge (final state of the product is not clear as yet, another has been bought out and been re-purposed, and another (Mendeley) has been having usability and reliability problems. Elsevier/Mendeley have also begun to encrypt the data in your library! This means you as the owner and organizer of the library are unable to move that data to another reference manager. Another has become superfluous. PaperPile and RefWorks work with GoogleDocs, but RefWorks is free to you as a UCSF person, and you pay a monthly fee for PaperPile. We try to monitor developments in reference managers and will provide information about significant updates.

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

These points refer to EndNote, F1000 Workspace, RefWorks, Zotero and Mendeley:

  • If you don’t want to pay for software, consider RefWorks (UCSF only), F1000 (UCSF only), or Zotero.
  • If you want open source software, choose Zotero.
  • If you want software that's easy to learn, choose RefWorks or F1000 (UCSF only). Zotero is pretty easy as well.
  • If you want to mainly work off-line on your own computer, EndNote is your best bet. Zotero is an alternative.
  • If you want easy online access to your references, consider RefWorks. EndNote Web/Online, and Zotero also permit this, but with fewer features than the desktop versions.
  • If you have saved a large collection of PDF files on your computer which you wish to add to your reference manager, Zotero, RefWorks, and EndNote are all able to add them to libraries, and extract the the citation data you will need when writing your manuscript.
  • If you want a program that will fetch batches of PDFs for you after you have added them to your library, EndNote is the best choice. Zotero does OK at this function.
  • If you are writing a systematic review or performing other research during which you will accumulate a large number of references (5000 or more) prefer EndNote.
  • If you have special requirements that will require extensive customizability, prefer EndNote
  • If you're interested in using the software to collaborate with colleagues, Zotero, RefWorks, EndNote are preferred.
  • If you want to sync your library with multiple computers, choose Zotero, RefWorks or F1000 (the latter two are online platforms).

This is an attempt to provide a brief overview of five popular citation management software. The right software for you will depend on your work and your environment.


Comparison table for EndNote vs. RefWorks

EndNote and RefWorks are the two most popular managers here at UCSF.





Desktop: Installed on computer

EndNote Basic: Free stripped-down version.

Ease of Use More customizable than RefWorks Easier to use than EndNote
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. Also works in GoogleDocs.
Windows/Mac Current version, X9 has minimized visual difference between the platforms.

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, depends on settings No

Store PDFs

Yes Yes, add one at a time

Ability to Annotate PDFs

Yes Yes, in Acrobat or other PDF reader

Create a Formatted List of Figures & Charts.

Yes No

Support for Mobile Devices (Android and iOS)

Not really.

New RefWorks does not have an app. Website is not mobilized.
Support for iPAD There is an EndNote X9 app in the App Store. 

You can access RefWorks with your browser on your iPad, functionality is limited.


On the desktop version, you can share folders with others using the share function, or export libraries others can add to their EndNote. EndNote web version is designed for sharing.

Share database (or folders) with members you invite.

More Information

EndNote FAQ

RefWorks FAQ