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Citation Management

Choosing a citation manager, tutorials, and more


October 13, 2022

Citation Management in the Cloud

Blog post detailing troubleshooting when collaborating or working with citation managers and/or word processors in the cloud environment.

Citation Mangers in the Cloud

EndNote Web

In 2007, EndNote released EndNote Web, a web-based version of EndNote that was integrated in ISI Web of Knowledge (today known as Web of Science). EndNote Web later became EndNote Basic (there are two versions) and EndNote Online.

  • EndNote Basic is a web-based reference manager that allows for up to a maximum of 50,000 references and 2GB of attachments. There are two different versions of EndNote Basic.
    • A free web-based only version of EndNote with limited functionality (21 citation styles and a limited number of filters and connection files). It requires no additional purchases, subscriptions, or licenses.
    • An upgraded version of EndNote Basic that is available to individuals who have institutional subscriptions to Web of Science. This version of EndNote Basic has thousands of citation styles and hundreds of filters and connection files.
  • EndNote Online is the cloud-based portion of the licensed EndNote Desktop. This online version of the desktop library can contain an unlimited number of references and attachments.
    • EndNote Online can only sync to ONE (1) EndNote Desktop Library, and from there users can share references and collaborate with others.
    • EndNote Online syncs with EndNote desktop versions: X8, X9 and 20.

The company Mendeley (named after biologist Gregor Mendel and chemist Dmitri Mendeleev) was found in London in 2007 by three German PhD students. It's first public beta version software was released in August 2008. From its inception it's focus was on open sharing and access, and it's software is freely available (up to 2GB of storage). In 2012 it was one of the original repositories set as "Green" Open Access (self-archiving of post-prints), however, that was revoked a year later when Elsevier bought Mendeley.

Since the acquisition by Elsevier, Mendeley has undergone a series of changes to its products and its functionality.

  • Mendeley Reference Manager is a free web and desktop reference management application. It helps you simplify your reference management workflow so you can focus on achieving your goals.
  • Mendeley Cite add-in for Microsoft® Word allows you to easily insert references from your Mendeley library into your Word document, change your citation style and generate a bibliography - all without leaving your document.
  • Mendeley Web Importer is an extension for web browsers which helps you to add references to your library with full text PDFs. We’ve rebuilt from the ground up to ensure you are always able capture the references you need.

NOTE: MSK InfoSec currently does not authorize installing Mendeley Cite on MSK workstations or MSK-issued devices.


Zotero is a web-based free (up to 300MB) and open-source reference management system. Zotero 1.0 was first released in October 2006 as an add-on to the Firefox browser. In 2017 Zotero 5.0 was released, which eliminated the Firefox plug-in, replacing it with a connector to it's new stand-alone product, the Zotero App.

Zotero Storage provides additional (purchased) online storage space for your Zotero files, allowing you to synchronize PDFs, images, web snapshots, and other files among all your devices, share your Zotero attachments in group libraries, and access files via your online library on


SciWheel, formerly F1000 Workspace, is a cloud-based suite of tools that includes reference management, writing, collaboration, and manuscript preparation. It was launched in 2015.

As of August 31, 2021, SciWheel will no longer be providing support for the original Word plugin & desktop app. If you already have this installed, you will still be able to use this plugin & desktop app after this date. SciWheel is now completely in the cloud.

  • The new Sciwheel browser extension is a powerful add-on available for most popular internet browsers. It allows you to save articles quickly and easily as you browse. You can add notes (highlights and comments) to web pages or PDFs, and add articles/web pages directly to Sciwheel. Members of a shared project can share their annotations making the process of collecting relevant references much more efficient.
  • With the new Sciwheel Word add-in you can easily cite any references saved in Sciwheel. You'll get smart citation suggestions and be able to search PubMed or expert recommended articles in Faculty Opinions without leaving Word.
  • With the new Sciwheel Google Docs add-on you can easily cite any references saved in Sciwheel. You'll get smart citation suggestions and be able to search PubMed or the 170,000+ expert recommended articles in Faculty Opinions without leaving Google Docs.

NOTE: MSK InfoSec currently does not authorize installing the SciWheel Word add-in on MSK workstations or MSK-issued devices.


RefWorks is a web-based citation management software, produced by ExLibris, a part of ProQuest. It was founded in 2001 and acquired by ProQuest in 2008. A Microsoft Word plug-in called Write-N-Cite allows users to add references from their library to a Word Document. In 2005 RefWorks introduced RefShare, which allowed users to share collections (no attachments) with others via a public URL.

  • RefMobile is a mobile interface that was launched in 2009
  • RefGrabIt is a browser extension for Firefox and Internet Explorer
  • In 2016 ProQuest launched New RefWorks, RefWorks 2.0 was rebranded as Legacy RefWorks

PaperPile is a web-based reference management system built out of Google Chrome using a browser extension. It was founded in 2012 and produced by PaperPile LLC. It has specific integration features with Google Scholar and Google Docs. Recently PaperPile also has iOS and Android apps.

  • PaperPile formats citations and bibliographies directly into Google Docs, allowing for collaborative editing of manuscripts
  • PaperPile can also import and export RIS (EndNote) and BibTeX files
  • PaperPile Word Plug-In -- BETA
    • Paperpile's citation plugin for Microsoft Word is now available for download on both Windows and MacOS

Productivity in the Cloud


Microsoft 365 (formerly Office 365) is Microsoft’s subscription-based suite of products, including the core Microsoft Office software (Outlook, Word, Excel, PowerPoint, etc), as well as many additional cloud-based business services such as Microsoft Teams, SharePoint, and OneDrive.

Many of the core office products in the 365 suite also include the current desktop versions of the office applications – currently Microsoft Office 2021. Office 2021 is also sold as a one-time purchase of the Office applications for a single computer. There is also an Office for the Web, which is a free version of the core Office applications that can be used right in the browser.


Google Docs is a cloud-based word processor included as a part of the free Google Docs Editor suite offered within their Google Drive service. The suite includes: Google Docs, Google Sheets, Google Slides, and more. It is freely available to anyone with a personal Google account, as well as a part of Google Workspace.

The Google Docs Editor suite is available through web, as well as through mobile apps (iOS and Android) and a desktop application for Google's Chrome OS.


Pages is the word processor developed by Apple for the iWork Productivity Suite. It runs on the macOS, iPadOS and iOS operating systems as well as in iCloud and on the web.

The only known software other than Pages which can open its files are Apple's iWork productivity suite through Apple's iCloud and LibreOffice. Windows users can view and edit Pages files using iWork for iCloud via their web browser. The iCloud system can also read Microsoft Word files and convert Pages files to Microsoft Word format.