From The APA Science Student Council

Selecting a reference manager

Reviews of Zotero, Mendeley and ReadBook.

By Elizabeth Necka

A graduate student’s best friend — anything that saves time and brainpower, right? Apply this to writing papers and you have reference managers. Maintaining good record of the articles that you commonly use improves efficiency. When reading papers, reference managers allow you to take notes on and annotate PDFs without first printing them out. By using reference managers, it is no longer necessary to maintain a system of printing papers and putting them in binders. Managers also make it easy to share articles with collaborators, and to format in-text citations and bibliographic references while composing a manuscript. Using a reference manager, changing citation formats to fit journal submission requirements is as simple as the click of a button.

Below, I review three of the most popular free reference managers, with consideration of their strengths and weaknesses.


Zotero is housed within the Firefox web browser and has a stand-alone desktop application for use with other internet browsers such as Google Chrome and Safari. Zotero so inconspicuously lightens your work load that you might forget it’s even there. When reading an article online, users simply click a small button in the address bar of their internet browser and Zotero automatically downloads and saves the PDF of the article and extracts all bibliographic information. Users can access Zotero either through their Firefox browser (Ctrl+Shift+Z) or by opening the stand-alone app. When writing a paper in Microsoft Word, Open Office or Google Docs, users can easily search for and add in-text citations, which automatically appear in the bibliography. These features allow users to maximize their efficiency while using Zotero without having to do much out of their normal routine (i.e., they do not need to learn how to use a new program). Additionally, there are many useful third-party apps for mobile devices which further encourage the seamless integration of Zotero with your natural work flow, such as “Scanning for Zotero” and “Bibup,” which enables you to capture bibliographic information by scanning a book’s ISBN bar code with a mobile device. 

Zotero is technically billed as a reference manager, but in many ways I would consider it a citation manager. The difference is semantic, but I think it is important nevertheless. Unlike some of the other reference managers, Zotero’s notes features are somewhat limited. Citations are treated as folders which contain the PDFs of the document and, as a separate file, any note files a user adds. Zotero lacks the ability to annotate the PDF itself. Notes are searchable, however, which provides a definite advantage to the frenzied researcher trying to remember “Now where did I read that again?” Simply type a keyword that you may have used in your notes in the search bar to find not only your note but also the article to which it is attached. For the most part, Zotero has limited access to the actual PDFs associated with a citation. Users must open the article in an external PDF viewer to read the actual document.

Bottom line: For the researcher who does not like to mark-up papers as he or she reads, but is looking for a sleek interface that seamlessly enhances an established work pattern, Zotero may offer the best solution.  


Mendeley and Zotero are similar in the ease with which you can save and store articles. Like Zotero, Mendeley has an extension for internet browsers which automatically imports PDFs and bibliographic information into the stand-alone program. Like Zotero, it also has a Microsoft Word citation tool which allows users to seamlessly add references to their documents. However, unlike Zotero, Mendeley’s stand-alone program allows its users to view, interact with and annotate PDFs within the program (user-generated notes are searchable, but in-text annotations are not). These notes, however, only appear as annotations on the actual PDF document when you view the PDF from within the Mendeley application unless you explicitly opt to export your citations. This may be an ideal feature if you want to have a clean copy of an article to share with collaborators and students, but may also be disconcerting if you do not want to be restricted to using the Mendeley program exclusively, but also want to keep track of your annotations.

Mendeley’s biggest strength may be that it allows researchers to easily collaborate and share documents. Researchers can create private “groups” of up to three people, which permit the sharing of documents and notes. Having a joint Mendeley library makes it easy for collaborators to edit citations as drafts of a manuscript pass between authors. Users can also create public “groups,” which allow an unlimited number of collaborators to join. However, these groups function more as reading lists, in that bibliographic information is shared, but PDFs and notes are not.

Bottom line: Mendeley may be best suited to the researcher who is already entrenched in a lab that uses the program (as this will aid in collaborations).


ReadCube is a new reference manager which allows users to access “enhanced PDFs.” In many ways, by providing these “enhanced PDFs,” ReadCube acts more like an academic personal assistant than a reference manager. In ReadCube, while reading a paper, you can easily find an article that the paper references with the click of one button. ReadCube also saves your institutional proxy log-on information so that you can even access articles that are behind a pay wall, as long as your institution is a subscriber to the journal in which the article is published. If an article still happens to be behind a pay wall, the ReadCube Access feature will allow access to it for 48 hours or an option to buy it for use (within the ReadCube app only) at steeply discounted rates. ReadCube users can even search PubMed and Google Scholar from within the program itself. Users can take notes on their PDFs as they read, and can later search within their own annotations. In my opinion, however, the best feature of ReadCube is its Daily Recommendations. ReadCube will search for and recommend articles that may be of interest to you based on the articles in your library and your previous article history. The recommendations are updated daily. Although I can speak only from my own experience, the articles that have been recommended to me have all been highly relevant.

ReadCube is the newest program on the scene, a position which endows it with some advantages and some disadvantages. Although ReadCube may be somewhat low on features, users can provide valuable input regarding features they would like to see developed and incorporated in the future. For example, the development team is already working on an IOS application equivalent (which is currently in post-production) and creating a “cited by” feature which would allow users to easily access all of the articles citing the paper that they are currently reading. This month, ReadCube is rolling out optional pay-for-service cloud sync capabilities and a Microsoft Word citation tool which will allow you to cite papers as you write (much like Mendeley and Zotero’s Microsoft Word Add-In). ReadCube is still in beta status, however, which means it may be suspect to bugs and glitches (for instance, when it is syncing and retrieving information from PDFs already on your computer, it requires you to manually resolve the citation information for many articles and sometimes fails to resolve duplicates automatically). ReadCube also does not allow sharing capabilities, and much of its functionality is restricted to use within the stand-alone program. 

Bottom line: ReadCube may be appealing to those who appreciate easy access to an article’s references and who enjoy receiving personalized recommendations of articles. 

Choosing a reference manager is highly personal, and can mean some adjustment in how you work. However, reference managers can make managing your citations much more efficient and can improve your productivity.