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Citing and Citation Managers


Citation managers (also known as citation management software, reference managers etc.),
are available to help you collect, organize, cite and share references and sources (e.g. full-text articles).

"Many students struggle when citing sources in their research papers and have turned to web-based citation tools in increasing numbers" (Homol, 2014, p.552).

Benefits of Citation Managers

Manually formatting citations can be very time intensive! Familiarizing yourself with a citation manager early in your academic career can help keep you organized and can save you large amounts of time by obviating the need to manually format your citations.
In addition to being a great tool for academic writing, citation managers can also help you collect, organize and store information sources for other purposes. 

Citation managers allow you to:

  • Manage all of your sources in one place.
  • Upload and store full-text PDFs and other file types for your sources.
  • Generate formatted bibliographies in desired format.
  • Install plug-ins for word processors that allow you to insert citations from the reference manager as you write.
  • Organize your references into meaningful collection folders that may serve a variety of purposes.
  • Share collections with colleagues to collaborate in private or open groups.
  • Facilitate the removal of duplicate citations.

How Citation Managers Work

Citations can be downloaded from library resources (Omni discovery tool or databases) and imported to citation managers individually or in bulk, or added to citation managers manually, however, this does not include the corresponding full text articles. Full-text articles and other files can be uploaded to corresponding citations afterwards. 
Some citation managers, like EndNote, Mendeley, and Zotero, offer web importer plug-ins that can be installed to your internet browser to capture citation information as well as the corresponding full text articles.
Additionally, Mendeley and Zotero give users the option to drag and drop PDF articles into the citation manager, which imports the associated citation information.

Choosing a Citation Manager

There are many different citation management programs available and many offer a freely available option. 

  • Choosing a citation manager that's right for you largely depends on the intended purpose and may be different for undergraduate students, graduate students and faculty members.
  • You may find it useful to consult with your peers and faculty supervisors to get their advice on appropriate software.
  • The three most popular citation managers, EndNoteMendeley and Zotero, all offer an online and desktop version and provide a freely available option. 
  • Queen's University has a site license for the subscription-based (desktop) version of EndNote
EndNote vs Mendeley vs Zotero
  • EndNote desktop is more advanced to use and might be better suited for graduate students and faculty/staff than undergraduate students. Mendeley and Zotero are relatively easy to use, in comparison, and more intuitive.
  • Unlike EndNote, both Mendeley and Zotero allow users to drag and drop PDF articles into the citation managers, which imports the associated citation information.
  • Mendeley and Zotero allow users to install web importers to easily grab and import citations from online without needing to download and import RIS files (which is necessary in EndNote).  
  • Zotero offers a plug-in for Google Docs

  • EndNote offers a journal matching feature, known as Manuscript Matcher, to help users find the right journal for their manuscripts.

  • EndNote and Zotero both integrate with the Retraction Watch database to provide retraction alerts for articles in your libraries. These appear in a separate folder called 'Retractions' or 'Retracted Items' and feature a brief description of the purpose for the retraction.
  • Mendeley offers additional social networking features in the online version. For example, users can search for and follow other researchers with similar interests and receive updates.



Key questions for choosing a citation manager:

Ease of Use / Usability

  • Do I like the interface? Is it intuitive to me?
  • Do I easily find the functions I'm looking for?

Operating system


  • Which software can I use with my operating system (Linux, Mac, Windows)?
  • Which software offers an online version?
  • Which software offers a mobile version/app?



  • Are there any training courses for beginners?
  • Are there any materials for self training (e.g. videos, manuals)?
  • Is there any support if I need help (library, company, IT hotline, forums etc.)?



  • What external programmes should my reference management software support (e.g. word processor)?



  • Does the software cost anything?
  • Is there a campus licence at my institution (university/company)?
  • Are there potentially additional costs (e.g. after leaving institution, need for more storage space)?

What features should my reference management software offer?

  • Searching for full text?
  • PDF editing?
  • Generating bibliographies?
  • Managing quotes / ideas?
  • Catalogue and database search from within the programme?
  • Indexing and structuring of content?
  • Online access?
  • Sharing and/or jointly editing references?
  • Task planning?
  • LaTeX support?
  • Retraction alerts?

Where do I usually work?


  • Do I use always the same computer or do I switch sometimes?
  • Do I have permission to install software on the computer I use?
  • What reference management software do my colleagues/collaborators use?

Adapted from Universitätsbibliothek der Technischen Universität München (2016). "Answers to many of the following questions can be found in the software comparison document. However, some question will be answered only by testing the programme yourself."

Comparison of Citation Managers

Detailed comparisons of citation managers can be found online and as published journal articles.

Table 1: Citation Management Tools at a Glance
Adapted from: Ivey, C., & Crum, J. (2018). Choosing the right citation management tool: EndNote, Mendeley, RefWorks, or Zotero. Journal of the Medical Library Association: JMLA, 106(3), 399.

  EndNote Mendeley Zotero
Platforms Mac, Windows Mac, Windows, Linux Mac, Windows, Linux
Browsers Internet Explorer (IE), Firefox, Chrome, Safari IE, Firefox, Chrome, Safari Firefox, Chrome, Safari
Browser plug-ins IE (Windows only) and Firefox (Windows and Mac) IE, Firefox, Chrome, Safari Firefox, Chrome, and Safari 
Mobile apps iOS (iPad only) Android, iOS None; mobile-friendly site available
Word processing integration Microsoft Word
(Windows and Mac)
Microsoft Word (Windows and Mac), LibreOffice (Linux, Mac, and Windows) Microsoft Word (Windows and Mac), Libre Office (Linux, Mac, and Windows), [now compatible with Google Docs as well]
Importing references Refer/BibIX, tab delimited, RIS, ISI-CE, filters for hundreds of databases BibTeX, EndNote, XML, RIS, Zotero library, txt, Ovid (Medlars reprint), PubMed/MEDLINE (nbib), Mendeley web catalog Bibliontology RDF, BibTeX browser bookmarks, Citavi 5 XML, CSL JSON, EndNote XML, MAB2, MARC, MARCXML, PubMed/MEDLINE (nbib), MODS, Ovid tagged, Primo normalized XML, PubMed XML, RDF, Refer/BibIX, RefWorks tagged, RIS, Web of Science tagged, XML ContextObject
Add reference by identifier Available by searching external databases in application ArXiv ID, DOI, PMID ISBN, DOI, PMID
Offline availability Yes, references and files stored locally Yes, references and files stored locally

Yes, references and files stored locally

Retraction alerts Yes, integrates with the Retraction Watch database To be confirmed Yes, integrates with the Retraction Watch database



Comparison of De-duplication Functionality

A recent research study evaluated the performance of default de-duplication settings in the citation managers EndNote desktop X9, Mendeley, and Zotero, as well as in systematic review software programs (see table below). For citation managers, Mendeley performed the best, followed by Zotero. 

EndNote X9 identified a lot of duplicates that were not true duplicates (false positives), and missed identifying many true duplicates (false negatives). If using EndNote X9, it is highly recommended that you review any duplicates identified before hitting the delete button. Unpublished data evaluating the performance of EndNote 20 with the same sample of references shows a substantial improvement compared to EndNote X9 (to be presented by Sandra McKeown at the Medical Library Association conference in May 2021).

If you need to de-duplicate large batches of search results for the purpose of conducting knowledge syntheses, it is highly recommended that you take advantage of the systematic review software program Covidence, which the library provides access to. 

Table: Accuracy, Sensitivity and Specificity of default algorithms for each de-duplication method, presented with 95% confidence intervals




EndNote X9

0.76 (0.75, 0.78)

0.57 (0.54, 0.60)

0.89 (0.88, 0.90)


0.93 (0.92, 0.94)

0.84 (0.82, 0.86)

0.99 (0.986, 0.995)


0.80 (0.79, 0.82)

0.52 (0.49, 0.54)

0.99 (0.98, 0.993)


0.96 (0.95, 0.97)

0.90 (0.89, 0.92)

1.00 (0.996, 1.00)


0.97 (0.96, 0.974)

0.96 (0.95, 0.97)

0.97 (0.96, 0.98)


Bhargava, P., Patel, V. B., Iyer, R. S., Moshiri, M., Robinson, T. J., Lall, C., & Heller, M. T. (2015). Academic portfolio in the digital era: Organizing and maintaining a portfolio using reference managers. Journal of digital imaging, 28(1), 10-17.

Courraud, J. (2014). Zotero: A free and open-source reference manager. Medical Writing, 23(1), 46-48.

Homol, L. (2014). Web-based citation management tools: Comparing the accuracy of their electronic journal citations. The Journal of Academic Librarianship, 40(6), 552-557.

Ivey, C., & Crum, J. (2018). Choosing the right citation management tool: EndNote, Mendeley, RefWorks, or Zotero. Journal of the Medical Library Association: JMLA, 106(3), 399.

Kali, A. (2016). Reference management: A critical element of scientific writing. Journal of advanced pharmaceutical technology & research, 7(1), 27.

Kratochvíl, J. (2017). Comparison of the accuracy of bibliographical references generated for medical citation styles by EndNote, Mendeley, RefWorks and Zotero. The Journal of Academic Librarianship, 43(1), 57-66.

Lorenzetti, D. L., & Ghali, W. A. (2013). Reference management software for systematic reviews and meta-analyses: an exploration of usage and usability. BMC medical research methodology, 13(1), 141.

McKeown, S., & Mir, Z. M. (2021). Considerations for conducting systematic reviews: evaluating the performance of different methods for de-duplicating referencesSystematic Reviews10(1), 1-8.
Nilashi, M., Dalvi, M., Ibrahim, O., Zamani, M., & Ramayah, T. (2016). An interpretive structural modelling of the features influencing researchers’ selection of reference management software. Journal of Librarianship and Information Science, 0961000616668961.
Salem, J., & Fehrmann, P. (2013). Bibliographic management software: a focus group study of the preferences and practices of undergraduate students. Public services quarterly, 9(2), 110-120.

Speare, M. (2018). Graduate student use and non-use of reference and pdf management software: an exploratory study. The Journal of Academic Librarianship, 44(6), 762-774.
Technische Universität München Library. (2016). Reference Management Software Comparison. 6th update. Available at: