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Citation Managers: An Overview

This research guide is being created to answer the most commonly asked questions and to allow you adequate time to transition your citations to another manager.

Which Manager is Right for YOU?

How do you know which program is right for you? Some things to think about when you choose:

  • Hanging out at the water cooler?  Chat with fellow researchers.  For example, if your colleagues are all using Zotero to share citations, you might consider Zotero so that you can share your research, too.
  • Keep an open mind and Use what you like!  No program is perfect 100% of the time, so use what you're comfortable with.
  • The sky's the limit in research, so don't be limited by using only one management software. Records can be transferred from one program to another, so don't feel pressure to choose only one.

Zotero vs Mendeley vs Endnote Comparison Chart





Endnote Basic


Desktop Software and Browser Add-on

Desktop Software and online account (with limited features)

Desktop (Endnote X9) or Web-based (Endnote Basic)

Where is my data stored?

Locally.  Web-based syncing capability between computers

Locally.  Web-based syncing capability between computers

Desktop (Endnote X9) or web interface (Endnote Basic)

How does it work?

Very intuitive.  Click the icon in the browser to add the item to your references.  Search and import records using PMID, DOI, or ISBN.  Extract citation information from PDFs.

Import information from many popular databases.  Extract citation information from PDFs.

Import information from many popular, compatible databases.

Ability to work offline?



No (Endnote Basic) and Yes (Endnote X9)


Free with 300MB of back-up storage. Storage & group upgrades available for a fee. Open source.

Free at this time; built and hosted by Elsevier

Available to purchase (Endnote X9) or Free to WVU Faculty, Staff and Students; built and hosted by Thomson Reuters (Endnote Basic)

Word –processing Compatibility

Desktop software and browser add-on for Firefox, Chrome, and Safari

Desktop software and web-based.  Works with IE, Firefox, Chrome, and Safari (javascript & cookies must be enabled)

Desktop software


Zotpress, Biblio Bouts, phpZoteroWebDAV, Scanner for Zotero, Zandy, Zotpad, Zotero, Reader, ZotSpip, Bibbase

PaperShip, KinSync, Altmetrics, Scopus, GBIF, BibBase, PLOS, labfolder, Overleaf, OSF, Hivebench, Peerwith, Kuary, and Impactstory


Importation Abilities


(Library catalog and databases, web pages)


(Library catalog and databases, web pages)


(Library catalog and databases, web pages)

Learning Curve?

Quick to learn; simple design, many online user guides and demos.

Quick to learn; Pretty simple interface.

Takes longer to learn, but not difficult with online user guides and demos.

Storage Capacity

300 MB (Free)

(Upgrade Options)

2 GB (Free)

(Upgrade options)

2 GB or 50,000 items

(Upgrade options)

Does it Back-up?

Yes if you choose to back up or sync your Zotero library. A small amount of storage for attachments is free 


(as an option)

Yes, to MyEndnote Online if you have an account

Attach Files

(PDFs, etc)


(option to attach automatically)


(can be highlighted and annotated)


Annotate PDFs (highlight & make notes)?



Yes (Endnote X9) and No (Endnote Basic)

Can you Export records to other citation software?






  • Easy to Learn
  • User Friendly Features (tagging, attachments, and notes)
  • Simple download for records
  • Great for managing PDFs and pulling citation metadata from PDFs
  • Easy Collaboration
  • Good for managing a variety of formats, including web pages.
  • Automatic citation extraction from PDFs
  • Downloads records from several databases that don’t work with other citation products
  • Easy Collaboration



  • Good Customer Support
  • Easy to work in multiple locations
  • Can handle large numbers of references
  • Can handle a large amount of references
  • Easy Collaboration

Mobile Site or app?


(Apple and Android options)


(Apple and Android options)

No (Endnote Basic) and Yes (Endnote X9)


Cited Works:  MIT Libraries (, The Pennsylvania State University (,, and