Academic Reference Management

Paul A. Beaufait, Prefectural University of Kumamoto; Richard S. Lavin, Prefectural University of Kumamoto


The nature of academic reference managers has changed over the years. Early on, a reference database would typically consist of a few tens of entries (bibliographic data only), entered manually. Academic researchers nowadays need to be able to assemble and have easy access to a wide range of resources, including journal articles, books, book chapters, websites, and more. They need to categorize these data with tags or keywords, arrange them in lists by project, and output them in reference lists. Many need access to their data on multiple computers, as well as phones and tablets, and some share data with co-researchers. This article describes currently available software to give you an idea of various options.

Options fall into two general categories: desktop-based and cloud-based tools. Those two categories overlap to a large extent with the following categories: paid and freemium. Most desktop-based software packages have evolved into their own mini-ecosystems that include syncing services and mobile apps. Similarly, cloud-based systems that originally operated wholly in browsers have recently spawned companion apps. A common advantage of desktop-based systems is a user-friendly interface following the conventions of host operating systems, while cloud-based systems tend to be more platform-neutral. An advantage of a cloud-based system is there is generally no initial financial outlay, and indeed users with modest storage needs may never need to pay. Conversely, once storage needs exceed free quotas, regular payments may be necessary to maintain access to your work.

The Main Choices

The authors have combined practical experience with all of the following desktop and cloud-based apps, except Docear and Citavi. We will mention institutional favorites EndNote and RefWorks here only in passing, since universities with subscriptions to these paid services generally offer ample information and training for faculty and students.

Desktop-based Applications

Bookends and Sente

These packages are proprietary, desktop-based applications available for Mac, with iOS companion apps. Bookends (, a single-developer application renowned for its frequent updates and excellent support, has been in more-or-less continuous development since 1983, when it was released for the Apple II+. Close ties with Mac developments allow for good usability and an extensive feature set. Sente ( is notable for having convenient note-taking features. Both have cloud services that enable easy sharing of databases among multiple computers. In the case of Sente, seamless syncing with iOS devices also is available. The flip side is that these apps are not available on the more popular Windows platform.


Papers ( is another proprietary desktop-based application. At first, it was exclusively for Mac, but the Mac version was followed by an iOS companion app, and it is now available for Windows. Papers pioneered convenient and interesting features, such as the ability to look up references for citing in a text document without having to launch the application. It has a clean and modern look that makes it a joy to use. 

Online and Beyond


CiteULike ( was one of the first online reference managers, and may be a good choice for those just getting started. One difference from other products is that CiteULike works online only—through a browser. Since the general public can access users’ public lists without registering, CiteULike is an option for one-way sharing of tagged lists of references for example: 

CiteULike also has a handy ‘groups’ function allowing teams of researchers or students writing theses on related topics to share information privately or publicly. 

Mendeley and Zotero

Mendeley ( and Zotero ( are major players in the cloud-based world of reference management. Beginning as browser-only software, Mendeley has released desktop versions for both Mac and Windows, and for mobile platforms, which allows users to sync online data among various devices. Mendeley groups can be private public (editable by invitation), or open. Zotero has standalone software for desktops and is served on mobile platforms by the third-party software PaperShip ( A standard usage pattern with these packages is that users will find articles for citation while browsing the web. Bookmarklets or browser extensions then allow users to capture relevant metadata, as well as associated PDFs—if they have access to the publications. Zotero is another option for one-way sharing of reference lists, with or without notes for example: 

With Zotero, users also can create private or public groups where members can share metadata and, optionally, PDFs.


ReadCube (, while being cloud-centric, feels radically different from Mendeley and Zotero. ReadCube is akin to Papers in look and feel, and more focused on individual users than collaboration. Through partnerships with publishing platforms, ReadCube offers enhanced PDFs in which it is possible to see full references associated with in-text citations without scrolling back and forth. One place to see ReadCube in action is in the Wiley Online Library (, if you have subscriptions to journals such as: Language Learning (Online ISSN: 1467-9922), The Modern Language Journal (Online ISSN: 1540-4781), or TESOL Quarterly (Online ISSN: 1545-7249).

Citavi and Docear

Citavi ( is a proprietary, Windows-only, desktop-based application that combines reference management with outlining and manuscript development as well as project management functions. The free version accommodates both individual users and teams working on up to 100 references, and payment activates built-in premium functions. Docear ( is a free, platform-neutral, desktop-based application available for Linux, Mac OS X, and Windows. Though not a major player, it has key differences from the software mentioned so far. Rather than compartmentalising reference management in general, and isolating each reference as individual items, it gives equal prominence to bibliographic entries, annotations of those entries, and freestanding memos while also providing visual representations of the inter-relationships between all items. Like Citavi, Docear provides manuscript creation functions within the software, yet is the only open-source option among tools mentioned in this article.

Working with Reference Management Software

Collecting, organizing, and annotating references are core functions which ideally meld seamlessly into the composition of academic papers.

Collecting References

If you are just starting your research, your focus may be on collecting new items from the web. With cloud-centric systems, you will usually do this in a web browser. Browser bookmarklets or extensions will attempt to extract metadata from websites, and optionally download relevant PDFs where access is available. Desktop-based systems use a variety of mechanisms. For example, Sente has its own internal browser with targeted browsing which marks what it recognizes as reference items with red dots; clicking on those dots imports the metadata. Our impressions are that Zotero, Papers, and Mendeley have the most comprehensive metadata detection functions.

If you have been doing research for some time but until recently have not felt a need for purpose-built software, you probably have numerous PDFs on your computer that you would like a software to file for you. Many recent journal articles have digital object identifiers (DOI) somewhere on their first pages which make it easier for software to extract metadata (including titles, authors, journal names and volumes, dates of publication, page numbers, and abstracts). For PDFs without DOIs, software can scan for recognizable strings like titles and authors that it can use as search terms. Each reference management system has its own strengths and weaknesses, often connected to the academic fields of the developers or founders of the system. Therefore, it may be best to start with a small number of papers, representative of those you are likely to work with and experiment with a few systems. In general, though, you are likely to find again that Zotero, Papers, or Mendeley offers the best metadata extraction from PDFs. With book chapters or presentations, however, you may not get consistently good results, regardless of the software you use.

Organizing and Annotating

For us, this is the most important part of working with reference management software. We recommend that you look for software that matches your preferred workflow, and, if possible, one whose interface is a pleasure to use. It should be easy to store quotations, and add both freestanding notes and notes on quotations. Ideally, it should also be possible to capture diagrams, figures, and tables in the same way as quoting text passages. Though most reference management software now offers tagging features, you should consider whether you prefer a hierarchical tagging system. Look at the searching, sorting, browsing, or filtering features to see whether they offer the options that you might need. For example: Can you search for items written by Carol Chapelle that have both “assessment” and “CALL” tags? Do you think that functionality will be useful?


Nearly all reference managers now offer some sort of cite-while-you-write features. Typically, these come in the form of plug-ins or other connections to word-processing software (e.g., EndNote to Microsoft Word, 2011+) so that when you reach a point in a manuscript where you wish to cite a specific reference item, you can invoke specific commands to insert in-text citations. Citations appear initially with a special markup that identifies them unambiguously to the software. When you have finished writing the manuscript, the software can scan the manuscript for that markup, reformat the in-text citations to match the reference style you have chosen (such as the APA, 6th edition), and list references at the end of the paper corresponding to the cited items. 

Those features may seem magical, but we would advise you to consider whether you really need them. Depending on details of feature implementation, switching between two applications may disrupt your focus, and you may find that a more hands-on approach suits you better. This can be done by inserting citations manually while writing, as you refer to a list of references in another column or window. Then you can generate formatted reference lists in the reference management software from items marked with manuscript-specific tags, and paste them into your manuscripts.

Closing Remarks

The conventional reference management paradigm has focused primarily on individual users working alone with single reference items, combined with quotations, notations, and associated files. Cloud-centric collaboration and cross-platform synchronization are now becoming de facto norms. Yet, while Bookends and Mendeley have made moves towards linking reference items to each other, at present it appears that only Docear and Citavi have made inter-linkage among references a central feature. That means that, for some users, they may replace outliners, mind-mappers, or other note-organizing applications. 

Wikipedia (n.d.), as you might expect, has tables of products, releases, and features—including supported import/export file formats and citation-style options for dozens of reference managers. Macademic ( has extensive coverage of reference management for the Mac. ThesisMonkey has produced a table comparing seven tools for thesis writing (2016a), and listed other informative sites (2016b). Albert (2015a, b) provided details on Docear. One consideration he emphasized was sustainability: If development ceases on your preferred software, what options will you have for exporting your data—not only PDFs, but annotations, too? 

The Bottom Line

Consider your budget, current workflow, and projected needs; try out a few of these reference managers (with colleagues or friends); and decide which works best for you.


Albert, S. (2015a). Sustainable research literature management with Docear:Part 1 [Web log post]. Retrieved from

Albert, S. (2015b) Sustainable research literature management with Docear: Part II [Web log post]. Retrieved from

ThesisMonkey. (2016a). Compare Endnote, ReadCube, Mendeley, RefWorks, Zotero, Papers, and Docear [Web log post]. Retrieved from

ThesisMonkey. (2016b). Why maybe a literature review is a good idea even when blogging [Web log post]. Retrieved from

Wikipedia. (n.d.). Comparison of reference management software. Retrieved from

Suggested Reading

University of Wisconsin. (2015, June 9). Citewog Flyer 2015. Retrieved from

Paul A. Beaufait and Richard S. Lavin work at the Prefectural University of Kumamoto in the Faculty of Administrative Studies and the Faculty of Letters, respectively. Both take great pleasure in leveraging available technology for collaborative cross-disciplinary research, teaching, and writing.