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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
  • Functions with many Web sites 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 Internet Explorer (IE) plug-in does not work well (tested with IE ver. 11)
  • The Capture Button does not work well with all partner websites
  • The Capture Button requires individual Web pages instead of a list of papers most of the time.
  • Aside from PubMed, the Capture Button usually only works on the search results screen (not a selected list) and you can't pick and choose items on the page. You must go to each page individually or import the entire list.
  • If it is not a partner Web site, 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
  • You can't have subscripts or superscripts if you need them
  • Some issues with the Android application and PDFs
  • It can pull in completely wrong data
  • It is possible that information like title, authors, etc. can't be edited and saved (mostly when in a group)
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.
  • You can't have subscripts or superscripts if you need them
  • 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 BasicFair. Fairly easy to edit individually. Not as easy to include PDF attachments. Easier if use at the beginning of your research before you have all your articles.
MendeleyFair. PDF drag and drop and editing is easy. Installing Plug in and Save to Mendeley button is easy. Some configuration is not obvious (e.g. configuring output fields). Group functionality is not intuitive. Can add notes and highlight PDF, fairly easy.
Zotero and Juris MFair. 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 that use the EBSCO interface (e.g. Academic Search Complete) have a direct export, but will require editing often. Editing is fairly easy
  • Most databases and import files don't pass the abbreviated and full journal titles as expected by EndNote Basic, so styles that require 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, but easy to edit
  • Can't be used with certain document types in particular citation styles because it does not have them (e.g. sound recording)
  • Has less fields than several other reference managers causing formatting problems for particular citation styles (e.g. conference proceedings, styles that use a database in the citation)
  • PDF Drag and drop doesn't work well for patents, thesis, and reports
  • Save to Mendeley Button does work well with all Web sites and databases
  • Books, patents and newspaper articles need entered manually most of the time
  • If you already have a document in your Mendeley database, often it will use the old data instead of the data in the RIS file
Zotero and Juris M
  • Many entries need edited, but easy to edit
  • Has the capability to be more accurate for conference proceedings and patents due to additional fields
  • Works well with many Web sites
  • Works well in the UA Libraries Catalog (best using book, DVD, etc. detail screen). Detects different types (e.g. DVD, Thesis) in the Catalog much of the time
  • Works well with databases, such as Hein Online, PubMed, database with the EBSCO interface
  • 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 Web site (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)
  • Manually Enter (if no other way)
  • PDF drag and drop (easiest, but will need edited). Works best for journal articles (depending on where you get it)
    • Digital Object Identifier (DOI) button in Mendeley Desktop can add information or it can load incorrect information and make it worse
  • Save to Mendeley button opens new window when can't use PDF drag and drop (easy)
  • Try RIS export if available when Save to Mendeley button does not work (fairly easy)
  • Manually Enter (if not other option)
Zotero and Juris M
  • Button integrated in Internet Browser (easiest)
  • RIS export if available and button does not work (easy)
  • PDF drag and drop (fairly easy). Get title, author, etc. by
    • using right-click menu and selecting Retrieve metadata for PDF/li>
    • Use Add Item(s) by Identifier button from the main menu
  • Manual Entry (if no other option)

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 SystemWindows 7 or later and Mac OS X 10.10 or later. Minimum system requirements for EndNote Basic opens new window. Not recommended for Linux.Mendeley Desktop is compatible with many versions of Window, Mac, and Linux. Minimum system requirements for Mendeley opens new window.Available for Mac, Windows, and Linux. 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.
BrowserCompatible with versions of Internet Explorer, Firefox, Safari, and Chrome. For more information, go to EndNote Online compatibility opens new window. Mendeley Web and the Save to Mendeley Button can be used with many versions of Internet Explorer, Firefox, Chrome, and Safari. Mendeley browser support opens new window. The Zotero Connector works for Chrome, Firefox, Safari, and Opera.
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.Not all plug-ins are compatible with Zotero 5 yet. If all your plug-ins work, use it; otherwise, use Zotero 4 Standalone. The firefox extension for Zotero 4 works better, but Mozilla is changing the how their plug-ins must be written and this extension will not work at some point. For more information about Zotero and Juris M, use the Zotero tab.
Use of Web version or download softwareNo Desktop versionDesktop and Web work together. You could not use important features if you did not install desktop and you have no choice but to create a login for the Web version.If you want to use Zotero on multiple computers, you will need to create a Web account on to sync with. 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. This makes the annotations 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, but some users say works with NVDA screen reader. 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.With any Mendeley user, but only one private group with two additional users with a free account. Problems with private groups like having to upload documents multiple times. Can create unlimited public groups, but cannot 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 online tutorials, guides, Mendeley support forum, and support team opens new window. Email available, but might take longer to respond.Documentation and forums on Zotero's page. Some universities have how-to pages and/or videos on YouTube.