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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 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 4 (EndNote, RefWorks, Zotero, F1000). There are many others available (relevant alternatives include Mendeley, PaperPile, Papers merged with ReadCube). As I write this in August 2019, Papers is now a subcription service costing $36/yr for students and $60/yr for academics, Elsevier/Mendeley began to encrypt the data in your library without your consent. Initially it was almost impossible to move your Mendeley library to another product but to their credit this problem appears to be resolved. Zotero, F1000, PaperPile and RefWorks work with GoogleDocs. RefWorks and F1000 are free to you as a UCSF person, Zotero is free to all unless you need to buy extra cloud storage space, Mendeley costs money is 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, 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 F1000 or RefWorks (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 and F1000. 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, F1000 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. You can do this with RefWorks but it is a 1 at a time process.
  • 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 (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, F1000, 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.