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EndNote, Zotero, and Other Reference Managers

Software which stores and organizes information for your education, research and clinical care

Sciwheel subscription ends June 30, 2021

UCSF Library Subscription to Sciwheel and Faculty Opinion will end 30 June 2021!

Sciwheel is a reference manager comparable to EndNote or Zotero. Faculty Opinion is an article recommendation service which alerts readers to articles of interest based on preferences set by the user.

Budgetary issues in the wake of COVID-19 require we make these cuts. Both products are excellent, but we cannot currently afford them.

Steps to move what you have stored in Sciwheel to Zotero or EndNote.

This handout will walk you through it. (see below for text)

If you need more information about EndNote or Zotero, see these class handouts and check for upcoming classes in Upcoming Events at



If you are looking for something like Faculty Opinion, we suggest these free solutions:

1. From any database you can save searches about topics of interest and have new articles from your search sent to your email or an RSS feed. Examples of databases include PubMed, Web of Science, Embase and many others. You will need to set up an account with the database for this to work. MyNCBI for PubMed is one example.

2. Google and Google Scholar will let you do the same thing using your Google account.

a. Google, use the page.

b. Google Scholar has a create alert icon.

This link will take you to information about creating good Google/Scholar searches.

There are commercial products to alert readers to new, relevant articles as well. Two are worth a look. Read by QxMD and BrowZine. Read is available as an app and as a web version. Set up an account, set preferences to link UCSF Library to your account. Set topic area, topics, journals in which you are interested in preferences. You will notification about articles meeting the criteria you set. See, or go to the App Store or GooglePlay to download the app.

We receive questions about BrowZine at UCSF. BrowZine works best if your institution has an account. UCSF does not, with the free version you will only receive alerts from open access journals. Like Read, BrowZine there are apps and a web page version.


What are they? What do they do?

All reference managers 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 stored information to add in-text citations and a reference list to a document you are writing, or to create a bibliography.

Reference managers vary in many details.

We will focus on EndNote, Zotero and Sciwheel. We will support and teach Zotero and EndNote in the future (written January 2021). There are other available reference managers. Relevant alternatives include Sciwheel, Mendeley, PaperPile, Papers (now merged with ReadCube), Citavi, RefWorks, and more.

As I write this in January, 2021, UCSF does not provide EndNote, you will need to purchase it. The best price is $114 for students and $219 for faculty and staff. Zotero is free to all unless you need to buy extra cloud storage space. UCSF Library subscribes to Sciwheel, and is free to you while at UCSF. Mendeley is free for basic use, and costs money if you try to share your article library between a group of more than 3 people. Papers is now a subscription service costing $36/yr for students and $60/yr for academics. You pay a monthly fee for PaperPile and it only works with Google Docs. Zotero, Mendeley, Sciwheel, and PaperPile work with GoogleDocs.

We try to monitor developments in reference managers and will provide information about significant updates in this library guide.

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

These points refer to EndNote, Zotero, and Mendeley:

  • If you don’t want to pay for software, consider Zotero.
  • If you want open source software, choose Zotero.
  • If you want software that's easy to learn, Zotero, and Mendeley are pretty easy to learn and use.
  • If you want to mainly work off-line on your own computer, EndNote is your best bet.
  • If you want easy online access to your references, consider. Zotero, and Mendeley. EndNote Web/Online also permits this, but with fewer features than the desktop version.
  • If you have saved a large collection of PDF files on your computer which you wish to add to your reference manager, Zotero, Mendeley and EndNote are all able to add them in bulk. To do so they 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 (5,000-10,000 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 is preferred. EndNote does this adequately. Mendeley charges for groups larger than 3. Note that sharing only works when sharing with someone else using the same software. There are more complicated ways to share between products.
  • If you want to sync your library with multiple computers, choose Zotero or Mendeley

This is an attempt to provide a brief overview of three popular reference management programs. The right software for you will depend on your work, your collaborators, and your environment.