Three Options for Managing References in Grant Proposals and Other Documents

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June 1, 2023

If you work on certain kinds of grant proposals, particularly proposals for research grants, you must cite sources that support your proposed solution and provide evidence of related work and data. Proposals for community-based projects often require references as well, such as citations to government reports, public datasets, or news articles. Proposal teams often struggle to create systems for organizing background research and correctly citing sources in their proposals. The result is that the decision of how to manage references is often not made until after the proposal is well underway, and the references are scattered across several locations. It’s much easier and less stressful if you decide at the beginning of the proposal process which tools and methods you will use. Doing so will help everyone working on the proposal, from the writers and subject matter experts to the reviewers and editors.

Several options exist for organizing references and adding citations to grant proposals or other documents, such as project reports and research papers. In this post, we are going to highlight three citation tools (aka reference managers) that we’ve used to collect references and create bibliographies for grant proposals. Two options can be used for free, and the third offers a free trial for 30 days. 

Before we discuss each tool, we want to give a quick overview of what a reference manager is and why you may want to add one to your proposal development toolbox.

WHAT IS A REFERENCE MANAGER?

A reference manager is a software program that allows you to organize and format your references. Reference managers typically share standard features, such as the ability to collect and format a list of citations before exporting them for use in programs such as Microsoft Word. Many reference managers also integrate with other software, enable collaboration, and allow content to be imported from various sources.

Many reference managers also allow you to search for relevant articles from within the tool and have features similar to a PDF reader (e.g., the ability to import and read PDFs, highlight text, and add notes). 

WHY USE A REFERENCE MANAGER?

If you are writing anything that requires background research, including grant proposals, a reference manager can be extremely valuable. Without one, you’ll have to collect your references in a Word document or something similar and, depending on the required style, manually format the citations before pasting them into your document. You’ll also need to find a safe place to store the reference list and copies of articles and other source material where they can easily be found, accessed, and shared. With a reference manager, you can do all of this—find relevant articles, add and format citations, read and annotate PDFs, and collaborate with others—using a single tool.

One of the main advantages of reference managers is that they make it much easier to insert and format citations. Scholarly journals, online news sites, and government agencies each use a specific style for referenced information. While the styles can be very similar regarding what information needs to be included, there are often nuances that are easy to miss in terms of the order in which the information should appear (e.g., date of publication before the name of the publisher or the other way around).  If you use a reference manager, you can use the software to search for and select the citations you need and automatically change the citation format to the required style. 

The ability to quickly change styles is reason enough to use a reference manager, especially if you have a long list of references that need to be formatted in an unfamiliar style.  Another benefit of a reference manager is that it can replace other Cloud-based storage options. Because many reference managers can be used to find and save full-text articles, you can use them instead of Google Drive or Dropbox for storing your background research.

If you’re thinking: But Microsoft Word has a reference tool—why not just use that? That’s a good question. The answer is that Microsoft’s reference tool is for formatting citations that you’ve added to your document. It isn’t a tool for conducting and managing background research or reading and annotating PDFs. However, if you need to add just a couple of footnotes to a proposal, a reference manager is unnecessary, and Word’s reference tool is fine. Still, even in that case, there may be a benefit to setting up a reference manager. If you do, you’ll be prepared to manage a more extensive list of references should the need arise when working on future proposals. Additionally, having a designated tool to collect and organize references can lessen the risk of data loss as a result of staff turnover. Instead of having references for various proposals scattered across personal files that will disappear when someone leaves, a reference manager allows reference lists to be accessible to several people in the organization, ensuring that past research will not be lost.

Overview of Three Reference Managers: Mendeley, Zotero, and Paperpile

Below, we summarize the key features of three reference managers—Mendeley, Zotero, and Paperpile—and suggest use cases for each. We chose these three because of their overall usability, features, customizability, and affordability.  If you’ve used reference managers in the past, you may be surprised that Endnote is not on our list. Endnote is the most well-known reference manager, and the only one many researchers would consider using. The reason we’re not profiling Endnote is that it is more expensive and thus out of reach for many nonprofits. However, Endnote has many features that make it particularly useful for large collaborative efforts, so it is worth considering if you can afford it. At the time of this writing, an Endnote license goes for $248 ($135 for students). Endnote offers a free trial period of 30 days. Endnote also has a free option called Endnote Basic, which comes with 2GB of storage and limited features.

MENDELEY 

Mendeley, which is owned by the publishing company Elsevier, offers many of the same core features as Endnote but offers more affordable subscriptions depending on your storage needs. For $55/year, you can get 5GB of storage, and if you need unlimited storage, you can move up to their Max plan, which costs $165/year. Mendeley also has a free plan that comes with 2GB of storage.

Like Endnote, Mendeley can be used for collaboration. If you are working on a grant proposal with others, you can create a group space for the proposal in Mendeley where you and your colleagues can add references and notes. Additionally, just like with Endnote, you can build a personal library in Mendeley where you can reference journal articles, content from the web, and imported PDFs. If you are writing your document in MS Word, Mendeley has an integration that allows you to add citations from your Mendeley library directly into your Word document. 

Mendeley’s features include:

• Automatically generating bibliographies

• Collaborating easily with other researchers online

• Importing papers from other research software

• Finding relevant papers based on what you’re reading

• Accessing your papers from anywhere online

Mendeley can be accessed online or through a desktop version. Mendeley also offers something called the Mendeley Web Importer that allows you to import references into your Mendeley account as you browse the web.

Who is Mendeley for? Mendeley is a good option if you want a single platform to organize references, read and annotate PDFs, establish a shared library with colleagues, and import citations into Microsoft Word. Mendeley’s free plan is perfect for those needing basic functionality and limited storage. Although it doesn’t integrate with Google Docs, you can still use Mendeley to find and organize references and export a bibliography to add to your document.

Mendeley allows you to access your library from anywhere: Windows, Mac, Linux, and all browsers.

ZOTERO

Zotero was launched in 2006 by an independent non-profit organization. Zotero stores your data on your computer, making it a good option if you are concerned about data privacy. However, please note that you will need to share your data with Zotero if you want to use its sync feature. 

Zotero takes time to master. To help new as well as more seasoned users, Zotero provides several resources, including a community forum where you can ask questions. Zotero also posts detailed user guides. Additionally, many university libraries have prepared resource manuals for Zotero. Often these resources are posted on public-facing web pages that anyone can access. 

Zotero offers several compelling arguments on why you should use its software over similar ones like Mendeley, Endnote, and Paperpile. One of Zotero’s points is that the other software programs are based on open-source software created by the Zotero community. Additionally, Zotero receives frequent updates, something not seen with other reference managers such as Mendeley.

Select Zotero features include:

• It’s free and open source

• Allows you to save data from websites, journal articles, newspapers, and more, including retrieving publication data for PDFs

• Offers word processor integration with Word, LibreOffice, and Google Docs to manage citations and bibliographies while you write

• Has a built-in PDF reader that lets you mark up PDFs and extract cited quotations and comments directly into notes or word processor documents

• Enables you to collaborate with others to build a bibliography

• Will automatically redirect you through your institution’s proxy so that you can access a PDF that is behind a publisher’s paywall

If you don’t want to create an account with Zotero or only need a simple bibliography, you can use ZoteroBib, Zotero’s free web-based tool for creating bibliographies.

Zotero’s desktop version is free to use. However, you will need to upgrade to a paid account if you want to use the sync function and need more than 300MB of storage. 

Who is Zotero for? Zotero is a good choice for someone who wants to have full control of their references. Unlike Mendeley and Paperpile, Zotero gives users the option of keeping their data private by using the desktop version of the program. Zotero is widely used in academia, so it is a good fit for students and faculty. Others may like Zotero because it receives frequent updates, is open source, and is a product of a non-profit organization. Last but not least, Zotero is feature-packed, so it’s also a good option if you want to go with a reference manager that offers high functionality and will keep up with your evolving needs as a writer and researcher.

Zotero works with Mac, Windows, Linux, and iOS. Because it is a program that runs on your computer, you must install Zotero on each computer that you want to sync to your online account. 

PAPERPILE

Paperpile came out in 2012. It was developed by three computational biologists during their time at the European Bioinformatics Institute and MIT.  We discovered Paperpile last year while working on a proposal for the National Institutes of Health (NIH) in collaboration with academics from several U.S. universities. Not all proposal team members could use Microsoft Teams, which we were planning to use as the workspace for the proposal. As a result, we switched to Google Drive, using Google Docs to develop the proposal. After finalizing the proposal, we converted it to Word for editing before submitting it as a PDF. Because we wanted to add citations as the draft developed, we initially chose Zotero as our reference manager because several team members had their references in Zotero, and Zotero offers a Google Docs integration. When we couldn’t get the Zotero extension to work, we looked for another option. That’s when we found Paperpile. Paperpile worked perfectly for finding and managing references and inserting citations into Google Docs. It also can be used with MS Word, so we were able to use it for all phases of our proposal’s development. In addition to using it to add citations to MS Word or Google Docs, Paperpile also integrates with Google Scholar, making it easy to find and import references into your reference library (you can also import data from PubMed and other publisher sites). At $36/year for personal or academic use or $120/year for business use, Paperpile is very affordable. While it doesn’t have a free tier, it does offer a 30-day free trial. 

Select Paperpile features 

• Uses the Google ecosystem 

• Collect references using the Chrome extension

• Organize your PDFs in Google Drive

• Cite references in Google Docs 

• Import data directly from Google Scholar

• Has a smart, intuitive interface

• Organize papers with folders, labels, and stars

• Look up papers online or search your library (Paperpile automatically imports the PDFs of the references you’ve added to your library)

• Fix references with incomplete data and clean up duplicates

• Offers the ability to share and collaborate with anyone (even those without a Paperpile account)

• Cite references in MS Word 

• Share copies of papers with colleagues 

• Annotate PDFs 

Paperpile works differently than the other reference managers in that it doesn’t offer a sync function directly through its service. Instead, if you want to sync your research to allow access across multiple devices, Paperpile uses your Google Drive account. If you currently use Google Drive for Cloud storage and have adequate space in your account, Paperpile may be ideal. If you don’t want to use Google Drive as your storage hub or your account lacks enough space to store the data (this might be unusual, but it can be an issue for some), Paperpile won’t be a good fit. Another connection to Google is that Paperpile uses your Google login, meaning that you don’t need to create a new username and password when setting up your account.

Who is Paperpile for? Paperpile is an obvious choice for those who use Google Docs for most of their writing. It’s also good for group efforts that require an easily accessible, Cloud-based workspace. Whereas not everyone has a Microsoft 365, Dropbox, or Box account—all popular options for sharing files—most people do have Google accounts, making Paperpile potentially a faster, easier way to manage and share data for a collaborative writing effort. Paperpile also makes it easy to access your research. If you download PDFs through Paperpile and choose to sync your Paperpile account with Google Drive, you can access your research directly through Google Drive without having to log into Paperpile first. Lastly, Paperpile has an intuitive interface, so it’s a good choice for those who want to jump in and use a reference manager without having to first embark on extensive training. Finally, another advantage of Paperpile is that it doesn’t require those collaborating with you to have a Paperpile account.  

Paperpile is a web-based tool. It is fully supported on Chrome for macOS, Windows, Linux, and Chrome OS and has been known to function with Microsoft Edge and the open-source Chromium browser. It works with Google Docs, MS Word, iOS, and Android.

WHICH REFERENCE MANAGER IS THE BEST?

All three reference managers are great options. Which reference manager might be best for you depends on factors such as how much data you have to store, whether you’ll be working with others, or if you need a specific feature such as compatibility with Google Docs. Mendeley is a well-rounded tool that works in most contexts, including proposals. However, Mendeley doesn’t have an integration for Google Docs. For Google Docs, Paperpile emerges as the leader. Paperpile has a well-designed interface, is one of the easiest reference managers to use, and is perfect for those working predominantly in Google’s ecosystem. If you work with people who use Endnote and want a free (or less expensive) option that has a similar look and feel, either Mendeley or Zotero would be suitable.

Although feature-filled, popular, and free—and developed by a non-profit organization that is sensitive to data privacy issues—Zotero is the reference manager least suited for the occasional user, which includes the majority of proposal writers. This is because Zotero takes some time to learn, with an interface that is less intuitive than Mendeley’s or Paperpile’s. However, it is a robust reference manager, and its free plan will meet the needs of most proposal writers. If you frequently collaborate with university students or faculty, you should be aware of Zotero and have a general idea of how it works. And if you work in an academic setting, we would recommend creating a Zotero account and taking a few tutorials so you’re ready to use it.

SUMMARY

Reference managers serve several functions. They can act as search engines to find relevant journal articles, books, and web-based content; function as a PDF reader; and be used to store and organize your references and import citations into your documents. 

There are many reference managers to choose from besides those profiled in this post. The key to finding one that will work for you is knowing the context where you will be using it the most (e.g., research papers vs. proposals, if proposals, which types of funders), and whether you will be collaborating with anyone. You’ll also want to review the list of citation styles each reference manager supports before you make your decision. This is particularly important if the documents you tend to work on require a citation style other than mainstream ones like the American Psychological Association or the Chicago Manual of Style. 

If you want to use Google Docs, Paperpile is ideal. If you wish to annotate PDFs and import web-based content such as blog posts into your library, Mendeley, Zotero, or Paperpile will all work. If you are working collaboratively on a document, ideally everyone on the team should use the same reference manager, so you may also want to consider your colleagues’ preferred tool. In an academic setting, you should be prepared to use Zotero, which is popular among faculty and students.

Workarounds exist if writing team members prefer to use different reference managers. If team members can’t agree on which tool to use for a particular research project or proposal, one solution is to periodically import project-related references from the other reference managers into the tool that the lead writer (or the editor) is most comfortable using. If cost is a significant issue for you and your colleagues, several reference managers offer free plans, including Endnote, Mendeley, and Zotero.

Lastly, one thing to keep in mind is that regardless of which reference manager you choose, you are not limited to using just one, and you don’t have to stick with your first choice. You can use multiple reference managers to see which one you like best, or choose one reference manager and switch later. Although it can be a hassle if you have lots of data, all reference managers we’ve seen allow you to export your data, which can then be imported into a new tool.  

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Additional information:

This post covers only a few of the reference managers on the market. Other reference managers include Citationsy as well as one offered by SciSpace (formerly Typeset). To see a comparison of reference managers, including the ones profiled in this post, check out this Wikipedia article: https://en.wikipedia.org/wiki/Comparison_of_reference_management_software.

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