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Referencing and Citation

Leveraging Reference Management Software


Nathan Boutin, Associate Editor

December 2021

Accurate references are an important part of manuscript drafting. They are the primary method of giving credit to other researchers and avoiding plagiarism, a topic that is covered at length in the LetPub Learning Nexus article Plagiarism in Scientific Writing: What It Is and How to Avoid It. As manually inputting references into a paper can be tedious, reference management tools exist so you can automate the process. Thus, these tools prove to be incredibly valuable when preparing your manuscript for publication.

Why use reference management software?

There are many benefits to using reference management software. First, it can be difficult to keep track of the numerical order of citations. References can easily end up out of order when adding new sections in response to peer review. Using software will automate the numbering process as you write, accurately citing references along the way.

Perhaps the greatest perk of reference management software is that they can automatically format in-text citations. Journals invariably have different referencing styles, such as author-date, superscript numbers, or numbers enclosed in brackets. You can learn more about the most common Ways of Citing the Literature on the LetPub Learning Nexus. If you need to submit your manuscript to a different journal after rejection, changing all the citations manually can be a frustrating task. A few clicks are all you need when using reference management software to format the entire manuscript, saving you valuable time.

Other benefits include being able to import citation information directly from PDFs or webpages. Some software can generate a bibliography, and nearly all services allow authors to save and search for references in an extended library, which is great when you have multiple papers that share references.

What management software to choose?

There are many reference management software options to choose from. The choice depends on what features are appealing to you, but other factors such as cost come into play as well. Below, we explore a few popular options.

Zotero – Zotero is a free, open-source project that is great for those who like customization and plugins for word processors such as Google Docs and Microsoft Office. It also integrates with browsers for a seamless experience and even has apps for mobile devices. However, because Zotero is open-source, it lacks any formal support or development. This means that bugs that crop up may not be addressed quickly, and the software may have a learning curve.

Mendeley – Owned and operated by Elsevier, Mendeley is another free option that boasts similar functions to Zotero. However, the storage limitation (up to 2 GB) incentivizes users to pay a one-time subscription fee. Mendeley is great if your research is contained mostly in PDF files because the software has an integrated PDF viewer that can generate citations by simply importing the file. Furthermore, Mendeley has one of the largest community platforms. Unlike Zotero, Mendeley no longer has mobile support. In March 2021, the mobile app was discontinued and removed from the App Store and Google Play.

EndNote – EndNote, which is developed by Clarivate, is a popular software that allows users to curate a large library of references. While EndNote does have a free option, its primary strengths are gated behind a paywall. This one-time cost, which scales based on the version you decide to purchase (and may even be covered by your university or institution), will grant you access to unlimited web storage, a desktop app, the ability to annotate and highlight PDFs, over 6000 citations styles, and more.

These are some of the most widely used services, but there are many others including Bookends, Bebop, Paperpile, and Wikindx.

The bottom line

Ultimately, what reference management software you decide to use is based on your personal preferences. We recommend taking a few out for a “test drive” before you commit, as the paid choices usually have free trials or starter packages. To learn more about referencing, feel free to visit the LetPub Learning Nexus Referencing and Citations category.

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