Citation Management

ManagerCostWord Processor PluginsBrowser ExtensionsOnline Storage
ZoteroFreeMicrosoft Word, LibreOffice, Google Docs, and a variety of other word processors and writing systemsChrome, Firefox, and Safari300mb for free, more (including an unlimited storage option) available for a fee.
RefworksFree via Stanford's site licenseMicrosoft Word and Google DocsInternet Explorer and Firefox
MendeleyFreeMicrosoft Word and LibreOfficeChrome, Firefox, Internet Explorer, Safari, and other web browsers.2GB for free, 100GB for free with Stanford institutional edition, other storage options available for a fee.
EndNote$99 through the Stanford Bookstore. A free web-based version is also available.Microsoft OfficeFirefox, Internet Explorer, Safari2GB with a free account, Unlimited with a desktop account


Zotero is a web-based, open source citation management tool that is designed to store and manage bibliographic references.
Free version information
Zotero can be downloaded with basic features for free, with free plugins available that add additional functionality.
Paid or Institutional Version Information
Zotero provides 300mb of storage to synchronize PDFs, images, web snapshots, and any other Zotero files among all your computers and to share your Zotero attachments in group libraries. Additional storage (including an unlimited storage option) can be purchased for an annual fee.
Documentation and Tutorials
Accessing full-text PDF
  • From Zotero's Preferences choose Advanced and add the following URL to the OpenURL/Resolver box:
  • Next, highlight a reference and click on the small green Locate arrow.
  • From the pull-down menu, choose Library Lookup to locate and download the article.
  • You can then drag and drop the PDF file onto the reference in Zotero.
Sending Citations from PubMed to a Citation Manager
  • Download the ZOTERO connector for your browser.  
  • Run your PubMed search, then click on the small, yellow folder icon in the upper right region of your browser (the first time you use it, you may see a small black "Z" in the folder icon) and select the references you want to download.
  • Note that this tool only displays the references on a particular webpage (default in PubMed is 20 per page).
  • To download all the references in a PubMed search, use the PubMed Send to pull-down, select File as the destination, change Format to XML, and save the file. 
  • From Zotero, choose File/Import and then follow the prompts to import your PubMed references.


The new RefWorks is ProQuest's web-based bibliography and reference management software that increases research productivity by simplifying the research process and providing online collaboration space. Researchers and their groups can gather, organize, read, cite and share their reference materials from any locations. There are two versions of RefWorks: "new" RefWorks and "legacy" RefWorks. If you are new to RefWorks, then you may want to start with the New RefWorks.
Free version information
Paid or Institutional Version Information
To get started with the RefWorks, either New or Legacy version, use your Stanford email to sign up for a new account.
Documentation and Tutorials
Accessing full-text PDF
Click on a citation in RefWorks, then click Find it at Stanford to access the full text. You’ll need to save the full text of each article individually to your computer and then drag the PDF icon of the article onto the corresponding saved citation in your account. 
Sending Citations from PubMed to a Citation Manager
  • Although PubMed does not have a direct export to RefWorks, it's possible to create a file in PubMed that can be imported into RefWorks.
  • In PubMed, after selecting the references to be imported into RefWorks, use the "Send to" drop-down and select "Citation manager."
  • After verifying the information, click "Create File". The file will be called 'citations.nbib' and be in your computer's downloads file.
  • PubMed search results
  • Drag the citations.nbib file onto the Import from a file area.
  • RefWorks upload
  • Select Import to add the references to RefWorks
  • RefWorks import
  • Select "Continue" and "ok".
  • Imported references will appear in Last Imported view of RefWorks.


Mendeley is a free reference manager and academic social network that can help you organize your research, collaborate with others online, and discover the latest research. It is an Elsevier product.  It can be used in a web-browser or you can download a desktop application. 
Free version information
Mendeley can be freely downloaded and provides 2GB of personal storage. 
Paid or Institutional Version Information
The Mendeley Institutional Edition provides 100 GB of personal storage, 100 GB of shared library space, up to 100 collaborators, and an unlimited number of private groups. Stanford Libraries currently provides the Mendeley Institutional Edition but is exploring options during AY 2018-2019. To initiate access to the Institutional Edition, click the "join this group" button on the Stanford Mendeley Group page.
Documentation and Tutorials
Accessing full-text PDF
  • If you use the Mendeley web importer plug-in from Mendeley's Tools menu, you can allow Mendeley to import freely available articles (vs those that are subscription based). 
  • For articles Mendeley is unable to import automatically, you can download them individually and then drag and drop PDF files directly into Mendeley, Mendeley will try to generate references from the metadata within the PDF.
Sending Citations from PubMed to a Citation Manager
  • From PubMed, select the references you want to download by clicking in reference "check boxes." You can also download all references by not clicking on any check boxes.
  • Next, in PubMed, choose Send to click on File, click on Format, choose MEDLINE and click on Create File.
  • Drag and drop the file into Mendeley to import your citations.
  • Alternatively, you can download the Mendeley web importer plug-in from Mendeley's Tools menu. 


EndNote is a software application that can organize references from literature databases like PubMed, retrieve articles automatically for those references, and then generate formatted bibliographies in thousands of different styles. 
Free version information
Free trial - Desktop version (all features)

EndNote Basic - web-based only (some features of desktop app not available)
Paid or Institutional Version Information
Documentation and Tutorials
Accessing full-text PDF
  • To automatically download multiple PDFs, highlight your references; choose References/Find Full Text. EndNote will try to retrieve PDFs for the selected citations.
  • If you’re off-campus, you need to add two URLs to EndNote’s Preferences to use the Find Full Text option. If you’re using the Windows version of EndNote, go to the Edit/Preferences/Find Full Text window.
  • Add the following URL to OpenURL Path:
  • Next, add the following URL to "Authenticate with…"
  • If EndNote is unable to automatically import the PDF, select a reference, then right click it and choose URL/Open URL Link to access the findit@stanford full-text finder window.   
Sending Citations from PubMed to a Citation Manager
  • From PubMed, select the references you want to download by clicking in reference "check boxes." You can also download all references by not clicking on any check boxes.
  • Next, in PubMed, choose "Send To," click on "File," click on "Format" and choose "MEDLINE," click on "Create File."
  • If you’re using Firefox, you’ll be asked if you’d like to open with an application, so choose "EndNote" to open the file directly.
  • Otherwise, download the file to your hard drive and use EndNote’s "Import" function by choosing "Import" and selecting the downloaded file, then "Import Option," then "Other Filters" and then ‘PubMed (NLM)."
  • You can then import the downloaded file. 

Sending to/Exporting from Covidence from Citation Managers

Covidence has a large knowledge base with answers to many queries regarding sending citations to and exporting them from Covidence.  
  • Importing References into Covidence ( 
  • If using RIS format, imports with files exported from the following reference managers are supported: 
    • Cochrane Registry of studies
    • EndNote
    • Zotero
    • Mendeley
    • Refworks
Exporting study lists to your Citation Manager from Covidence