All about Reference Management Tools


Reference management tools are software programs that can help organise and cite references for academic writing. They serve as “virtual libraries” in which you can store hundreds of references to published papers that contain all of the relevant publication information, such as author names, journal names, volume, issue and page numbers. These reference databases are searchable, meaning you can quickly and easily find the paper you’re thinking of by entering a few key search terms. They are also invaluable tools when it comes to preparing a scientific manuscript for publication.


Advantages of using a reference management tool

One of the most significant advantages of using a reference management tool when writing your manuscript is that it avoids the errors that can arise when in-text references are inserted manually.


Consider, for example, that you have inserted references into your manuscript text manually in numerical order. In response to the peer reviewers’ comments, you then add a new paragraph in the middle of the Discussion that cites five additional papers. If the references have been inserted manually, you will then need to renumber all of the subsequent references to maintain numerical order, and it is exceedingly easy to introduce errors at this step, for example by overlooking a single in-text reference, especially if some papers have been cited more than once at different points in the text.


Using a reference management tool eliminates this problem by automatically updating reference numbering as you write, so you can feel confident that all papers are cited accurately in the main text of your manuscript.


Another key advantage of reference management tools is that they automatically format both in-text references and the reference list for you based on the format that you have selected.


For instance, some journals require in-text references to include the author name and sometimes year of publication (e.g. “Ramzy, et al.” or “Ramzy et al., 2012”), while some require a number in brackets or a superscript number (e.g. [5] or 5). While these references would be extremely time-consuming to reformat manually, when using a reference management tool this can be accomplished with the click of a button.


Similarly, formatting guidelines for reference lists can vary tremendously from journal to journal, and typing references out by hand and revising them to match a journal’s requirement takes valuable time away from more important tasks. Reference management tools offer huge time savings here, as you can simply select the format you wish to apply to the list, and the program makes the necessary changes quickly and accurately. Helpfully, many journals actually provide downloadable “style files” of their preferred in-house reference format that can be uploaded to your reference management tool, to ensure that the style you are using is as accurate as possible.


Choosing a reference management tool

There are a variety of reference management tools available, so how do you know which one to choose? Consider the following key features, which can help you select the right reference management tool for you:

  • Cost: There are both free and paid reference management tools. Clearly, a free option will be preferable for most users, but we suggest reviewing the features that these tools provide to make sure that they include all of the functions you expect to use or need. Keep in mind that some research institutions and universities have institution-wide subscriptions to paid reference management tools, so you may actually be able to use a paid program with no direct cost to yourself.
  • Number of users: Some reference management tools are intended for a single user, whereas others allow a reference library to be shared with multiple users. The option to share a library can be really useful if, for example, you wish to collaborate with your co-authors on writing a paper together, of if you want all of your lab members to be able to access and use the same master database. That being said, a single-user version could also meet all of your needs, depending on how you intend to use the software. 
  • Working style: One key feature that differs between reference management tools is whether they are intended for use on a single device (computer, tablet or otherwise), or whether they can be accessed online. If you primarily work only from your professional laptop, for example, a downloadable single-device version might be the best fit for you. However, if you often work on multiple devices, such as at work, from home and on-the-go, a program with online capabilities is likely to be more suitable, as it will sync as needed and allow you to work more flexibly.
  • File type: Finally, consider whether you work exclusively in Word or need the option to use your reference management tool with another program, such as LaTeX. Not all reference management tools work with a wide variety of file types, so we recommend checking a program’s ability to integrate with your desired word processing program.

Examples of commonly used reference management tools

Some of the most commonly used reference management tools are the following:

  1. RefWorks: RefWorks is a paid program that can be accessed through either a personal or an institutional account. Libraries can be shared with collaborators and synced with Dropbox. Furthermore, the tool works with both Word and GoogleDocs.
  2. Mendeley: Mendeley is a paid tool that can be used with Word (including Word for Mac), LibreOffice and LaTeX. It can be accessed from your desktop, online, or using the mobile app. In addition, it can be synced, and libraries are backed up in the cloud.
  3. EndNote: EndNote is a paid reference management tool that works on both Macs and PCs. It can be accessed from a computer or tablet, as well as online. The libraries created using this tool can be shared with collaborators, and there is an option to share only parts of a library, as well as tracking changes made by your collaborators.
  4. Zotero: Zotero is a free option that works with Mac, PC and Linux operating systems. It can be used to insert references and create bibliographies for papers written in Word, LibreOffice and Google Docs. In addition, it can by synced between devices and used online, and allows reference libraries to be shared between an unlimited number of users.
  5. Papers: Papers operates on a monthly subscription basis. It can be used with a standard desktop or laptop computer, as well as on mobile devices such as tablets and smartphones, and online. Reference libraries generated using this tool can be shared with a limited number of additional users, and libraries can be synced across devices.

End note

If you’re still unsure which reference management tool is right for you, you may wish to consult this comparison table published by the University of Chicago that compares the various features of Mendeley, EndNote and Zotero.



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