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Reference Management Tools: What reference manager to choose?

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Keeping your References and Notes Organized opens in new window discusses how to choose a reference manager. Also, it discusses three reference managers in-depth, where you choose one of them to try. A reference manager helps you keep your references and notes organized, which will help you when you start writing your paper.

Comparison Diagram

Details are in the Comparison Table

Best to Use When...

This table describes when it is an advantage to use a particular reference manager.
EndNote Basic
  • You are just starting your research
  • You are a Microsoft Word user
  • You mostly use Web of Science and PubMed
Mendeley
  • You already have all your PDFs and you want to search them full text
  • You want to put notes directly on the PDFs easily (need to export if want outside of Mendeley)
  • You use LibreOffice and/or Linux
  • Use your mobile phone much to get references
Zotero and Juris M
  • You need to use Bluebook Style or legal citations
  • Use many different websites and databases
  • Use a lot of conferences, artwork or sound recordings
  • You use LibreOffice and/or Linux.
  • Can search PDF annotations (with plug-in)

Disadvantages and Known Issues

This table lists some problems or disadvantages for reference managers.
EndNote Basic
  • You can't alter or create citation stylesheets
  • The Capture Button does not work well with all partner websites
Mendeley
  • Mendeley Web Importer can't always get the reference information
  • When pulling in a PDF to Mendeley Desktop, information needs edited most of the time, but it is easy to edit
  • It can pull in completely wrong data
Zotero and Juris M
  • When using the Zotero button with your Internet Browser, information needs edited most of the time, but it is easy to edit
  • Might take extra time to figure out plug-in is needed, but the documentation is excellent

Comparing Reference Managers

This is table list system requirements, software installation, and some general features.
EndNote BasicMendeleyZotero and Juris M
Can still use after graduationyesyesyes
System RequirementsNot recommended for Linux. For browser compatibility information, go to EndNote Online compatibility opens new window.Mendeley Desktop is compatible with many versions of Windows, Mac, and Linux. Mendeley Web Importer can be used various versions of common browsers. Minimum system requirements for Mendeley opens new window.Available for Mac, Windows, and Linux. The Zotero Connector works for several versions of common browsers. Zotero System Requirements opens new window.
Word processingPlug-in for Microsoft Word.Plug-in for Microsoft Word and LibreOffice.Microsoft Word and LibreOffice. There are numerous plug-ins for Zotero and Juris-M. For more information, use the Zotero tab.
Install softwareNot required, but Cite While you Write plug-in recommended. Capture works better with some partner websites than others. For a list of partners regarding the capture button, go to EndNote Online Help - Capture opens new window.Must install Desktop. Plug-in and the Mendeley Web Importer are recommended.Must install Zotero 5 and the Zotero Connector for your browser. Plug-in for Word or LibreOffice is recommended. For more information, use the Zotero tab.
Use of web version or download softwareNo Desktop versionDesktop and web version work together. You must create a free account on mendeley.com and download Mendeley Desktop.If you want to use Zotero on multiple computers, you will need to create a web account on zotero.org. If you don't save to zotero.org, you have to back-up your library manually.
Amount of space2GB for attachments and 50,000 references. 2GB300MB, but you could backup your PDFs to dropbox or Google Drive instead.
Full text search PDFsnoyesyes
Add notes to PDFsnoyes (visible in Mendeley only unless export). Notes in the PDF are not searchable.The plug-in Zotfile makes the notes in PDFs searchable.
ADA compliantThere is a Voluntary Product Accessibility Template (VPAT) for the full version of EndNote; however, all functionality for the web portion is listed as not applicable. There is not evidence that it was tested by the vendor. Go to accessibility information from vendor opens new window.There is a VPAT from Elsevier (PDF), opens new windowbut that is no replacement for testing yourself.No VPAT from vendor, the Zotero Forums have information about screen readers opens new window.
Citation StylesMany citation styles, but can choose 25 at a time only because the library subscribes to Web of Science. Once you graduate, you might have access to 21 styles only.Thousands of citation styles with the two latest edition of APA, Chicago, and MLA.Thousands of citation styles can be downloaded from the Zotero Style Repository opens new window. There are multiple editions of common styles.
SharingCan share folders with other EndNote Basic users giving them read or read/write privileges.Can create one private group with two additional users with a free account. Can create unlimited public groups, but can't include PDFs.Zotero groups has no limit on how many members may join your public or private groups. For more information, go to Zotero groups opens new window.
Searching external database directlyyesnono
Technical supportMuch of the online material is for those that purchase EndNote, so look for EndNote Basic first. There is support available. For more information, go to Endnote Online Guide opens new window. Mendeley has a support center. opens new windowDocumentation and forums on Zotero's website. Some universities have how-to pages and/or videos on YouTube.