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EndNote, Zotero and Other Reference Managers

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

Update on RefWorks status at UCSF

We will be ending UCSF Library's long time subscription to RefWorks on 6/30/2020. For RefWorks users we suggest changing to EndNote or Zotero as alternatives. We are seeing persisting problems with RefWorks integration with Chrome and Word. Without those integrations, RefWorks is not very useful. We can help you move your information to another Reference manager adn provide training to get you up and running with Zotero or EndNote. Please contact for questions.


Moving your RefWorks library to Zotero or Endnote is a simple process:

This document shows detailed steps:

This video walks you through the same steps: 

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 in a useful way and make it searchable.

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

They vary in many details.

We will focus on 2 (EndNote, Zotero). These are the two products we will support and teach in the future. There are others available (relevant alternatives include Sciwheel (previously F1000), Mendeley, PaperPile, Papers (now merged with ReadCube), Citavi, etc. As I write this in March, 2020, Papers is now a subscription service costing $36/yr for students and $60/yr for academics. Zotero, Mendeley, F1000, and PaperPile work with GoogleDocs. Sciwheel is free to you as a UCSF person, Zotero is free to all unless you need to buy extra cloud storage space, Mendeley costs money if you try to form a group of more than 3 people. 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, Sciwheel, Zotero and Mendeley:

  • If you don’t want to pay for software, consider Zotero or Sciwheel (UCSF only).
  • If you want open source software, choose Zotero.
  • If you want software that's easy to learn, choose Sciwheel (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 Sciwheel. Zotero abd EndNote Web/Online 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, Sciwheel and EndNote are all able to add them in bulk 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 is also good at this function.
  • If you are writing a systematic review or performing other research during which you will accumulate a large number of references (5,000 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 and Sciwheel are preferred. EndNote does this adequately.
  • If you want to sync your library with multiple computers, choose Zotero or Sciwheel (the latter is an online platform).

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.