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Reference Management Tools: What reference manager to choose?

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
  • 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
  • Cite many conference papers
  • Use many different websites and databases
  • You use LibreOffice and/or Linux.
  • Can search annotations (with plug-in)
  • Support for many mobile devices

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
  • Aside from PubMed, most of the time you can't pick in a search results list using the Capture Button. You must go to each page individually.
  • If it is not a partner website, the Save to Mendeley Button often can't pull 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

Ease of Use

This table lists some general observations about how easy it is to use reference managers.
EndNote BasicFairly easy to edit individual entries, but not as easy to include PDF attachments as the other managers in this comparison.
MendeleyDragging and dropping PDFs and installing the Save to Mendeley button are easy. Adding notes and highlighting information in PDFs are easy. Installing and using the word processor plug ins are easy. Group functionality and some Mendeley desktop configuration are not intuitive.
Zotero and Juris MSome of the functionality listed for Mendeley is slightly less intuitive in Zotero, but documentation is easy to find and helps when something is not intuitive.

Notes about Accuracy

This table lists some general observations about accuracy of the reference managers.
EndNote Basic
  • Works best with PubMed and Web of Science requiring the least editing
  • Databases like Academic Search Complete have a direct export, but will require editing often
  • Styles that use abbreviated titles are less accurate
  • Produces Chicago Style poorly
  • Has many more document types, so it has the potential to be more accurate. Unfortunately, it doesn't seem to utilize all types well
  • In general, most entries need edited
  • Doesn't have as many types as the other managers in this comparison (e.g. sound recording)
  • Can be less accurate for particular citation styles because there aren't enough fields
  • PDF Drag and drop doesn't work well for patents, thesis, and reports
  • Save to Mendeley Button does work well with all websites and databases
  • Books, patents and newspaper articles need entered manually most of the time
Zotero and Juris M
  • Many entries need edited
  • Has the capability to be more accurate for conference proceedings and patents due to additional fields
  • Works well with many websites and the UA Libraries Catalog
  • Works well with databases, such as Hein Online, PubMed, and Academic Search Complete
  • Manual entry is necessary for Lexis and Westlaw

Loading Documents

This table lists the different ways to get references in reference managers.
EndNote Basic
  • Direct export from a database or website (easiest). [e.g. Academic Search Complete and Web of Science]
  • When direct export isn't available, try the following. Choose the one that works best for you.
    • Capture Button works better for some partners than others (easy)
    • Online search in EndNote Basic (easy)
    • Export a file, then import into EndNote Basic (fairly easy)
  • Manual entry
  • PDF drag and drop works best for journal articles (easy)
    • Digital Object Identifier (DOI) button in Mendeley Desktop might add information
  • Save to Mendeley button opens new window can be used when you don't have the PDF (easy)
  • Can use RIS export or manually entry
Zotero and Juris M
  • Button integrated in Internet Browser (easy)
  • PDF drag and drop (fairly easy). Get title, author, etc. by
    • using right-click menu and selecting Retrieve metadata for PDF
    • Use Add Item(s) by Identifier button from the main menu
  • Can use RIS export or manual entry

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
Operating system and browserMinimum system requirements for EndNote Basic opens new window. Not 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 and the Save to Mendeley Button 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. Compatibility Matrix for Zotero 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 Web sites 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 Save to Mendeley button 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 and are both required.If you want to use Zotero on multiple computers, you will need to create a Web account on If you don't save to, you have to back-up your library manually.
Amount of space2GB for attachments and 50,000 references. 2GB300MB
languagesEndNote Basic interface available in 8 languages. The bibliographies cannot be automatically generated in other languages.The Desktop interface and the Mendeley Web interface are only available in English. You can change the bibliography in 50 different languages though.Can import, store, and cite items in any language. You can change the language of the user interface too. For more information, go to supported languages in Zotero documentation. opens new window
Full text search PDFsnoyesyes if install the plug-ins, pdftotext and pdfindex. You might need to rebuild the index for existing unindexed PDFs.
Add notes to PDFsnoyes (visible in Mendeley only unless export). Notes are not searchable.If you annotate a PDF in another program like Adobe Reader, you can import the notes into Zotero with the plug-in, Zotfile making the notes 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.No VPAT from vendor.No VPAT from vendor, the Zotero Forums have information about screen readers opens new window.
Versions of StylesMany citation styles, but can only choose 25 at a time.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.One private group with two additional users is available 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. Much of, but not all of, EndNote Online will be relevant. There is technical support available. For more information, go to Endnote Online Help opens new window. Mendeley has a support center. opens new windowDocumentation and forums on Zotero's page. Some universities have how-to pages and/or videos on YouTube.