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Choosing a Citation Manager

The following popular citation managers provide the same basic features and functionality with some exceptions. Below are a few scenarios that might be helpful when choosing a citation manager. Once you have narrowed down the choices, the rest is personal preference. Some tips: Consult the comparison chart below for specific features. Talk to people in your department – some disciplines tend to use one tool more than others. Consult your liaison librarian for a recommendation. 

Citation Management Software

RefWorks 3 (New) Logo

RefWorks 3 (New)

RefWorks 3 (New) is a web-based citation management tool that is available to students, faculty, and staff at participating universities, colleges, and health institutes. RefWorks 3 (New) can help you:

  • Collect references while you research in popular databases like PubMed and EMBASE
  • Store and organize your references in a personal account online, accessible anywhere
  • Cite your papers in Microsoft Word and create bibliographies in thousands of output styles
  • Share your references and collaborate with your colleagues

... and much more! We've created a research guide to where NYMC users can review the basic functions and features of RefWorks 3 (New). 

RefWorks 2 (Legacy)

RefWorks 2 (Legacy) is web-based software which allows you to create a database of references, manipulate, organize and share the database, and use those references when writing papers. It is licensed by the Health Sciences Library for use by the New York Medical College community.

We've also created a research guide to where NYMC users can review the basic functions and features of RefWorks 2 (Legacy). 

EndNote Desktop X9 Logo

EndNote Full (Desktop)

EndNote Full is a desktop reference manager software program that allows you to collect and organize your references and to create bibliographies. It allows you to either type in or capture references from our Electronic Resources.  Using EndNote, you can create bibliographies within Microsoft Word or other word-processors. EndNote is able to format bibliographies in almost every conceivable bibliographic citation style, such as APA, Chicago Manual of Style, MLA, Turabian, Science and other journal-specific bibliographic citation styles.

NOTE: The library does NOT offer copies of EndNote Full (Desktop) software.

EndNote Basic Logo

EndNote Basic (Web)

Endnote Basic (formerly Endnote Web) is a free version of EndNote available for institutions which subscribe to ISI Databases, like Web of Science. HSL subscribes to Web of Science, which can be accessed from the databases page.  Besides being free, the major advantage of EndNote Web is that you can access your account from any computer that has an internet connection (as long as you can access the NYMC Library's electronic resources).

Many users like to try out EndNote Web to see if it will meet their needs before they purchase the regular EndNote software. With EndNote Web, it is possible to share libraries with other EndNote Web users - making collaboration easy. EndNote Web can also work with EndNote so you can move references between the two (version 10 or higher).

Mendeley Logo


Mendeley is a tool that enables you to manage citations and PDFs using a desktop client or through your account on Mendeley also includes plugins for Word or OpenOffice, so you can easily create citations and/or bibliographies as you write your papers.

What makes Mendeley unique is that it enables you to leverage the power of social networking to create a global citation management network. Use Mendeley to connect with other researchers in your field and discover what they are reading. There are also groups you can join that focus on particular subject areas or research projects. Mendeley even allows you to log in using your Facebook account.

Setting up Mendeley is free and comes with 2 GB of storage on their web server. You can pay an additional monthly fee you to get more storage space. Learn more about pricing & storage here.

Zotero Logo


Zotero is a free, open-source research tool that helps you collect, organize, and analyze research and share it in a variety of ways. Zotero includes the best parts of older reference manager software — the ability to store author, title, and publication fields and to export that information as formatted references — and the best aspects of modern software and web applications, such as the ability to organize, tag, and search in advanced ways. Zotero interacts seamlessly with online resources: when it senses you are viewing a book, article, or other object on the web, it can automatically extract and save complete bibliographic references. Zotero effortlessly transmits information to and from other web services and applications, and it runs both as a web service and offline on your personal devices.

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Citation Management Software Comparison Charts

I Need to... Use  Why from multiple computers or locations.



EndNote Basic


Zotero saves your citation library to your local computer, but syncs with multiple computers so you can work from home, work, or school.
Mendeley is a program that lives on your local computer, but syncs with a web account.
EndNote Basic is entirely web-based and can be accessed from any computer with internet access, and can sync with EndNote desktop.
RefWorks is entirely web-based and can be accessed from any computer with internet access. without an internet connection.




ZoteroMendeley and EndNote store your citation libraries locally on your computer.
...archive web pages and import citations from sites such as Amazon and ArtSTOR.


Zotero allows you to easily save snapshots of web pages and annotate them within your citation library. It is a great tool for scraping citation information from web-based publications and some commercial and social networking sites. on a group project or share my citations with others.



EndNote Basic


Zotero allows you to share your citations through shared folders -- you can give individuals or groups permissions to add and edit the citations in the shared folder. Mendeley allows you to share citations and documents with a group of up to 2 other users, or create a public reading list that is open to all. EndNote Basic allows you to create and share groups with other users. RefWorks allows you to share your citations through shared folders by inviting up to 10  individuals and giving permission to read, annotate, or modify the entries.

Last updated February, 2016

Criteria Zotero Mendeley EndNote Full EndNote Basic RefWorks 3 (New)
Web based? Yes, works with Firefox browser and can sync with online account; connectors for Chrome and Safari available Not primarily, but can sync with an online account which is editable Yes, with EndNote basic account Yes Yes, entirely web-based
Must be online? No No No Yes Yes
Cost Free for basic account, some cost for more online storage space Free for basic account, some cost for more online storage space $$, Student discount through computer store Free Free when register with with NYMC email address. Keep your access after graduation
Word-processor compatability MS Word, Open Office, Google Docs MS Word, Open Office, LaTex MS Office, Open Office, iWork Pages MS Word Google Docs, Microsoft Word
Import from databases Yes Yes Direct export from specific databases Yes Yes
Import citation info from web pages Yes, also archives the page and you can add annotations Yes, with a bookmark for a limited number of sites (mostly publishers or databases) Yes, with Web Capture tool and EndNote basic account Yes, with Web Capture tool Yes with the Save to RefWorks tool for your browser
Storage capacity Unlimited local storage and data syncing; 100MB free Zotero file syncing (larger syncing plans available for purchase); or can use WebDav Unlimited local storage and data syncing; 1GB personal and 100MB shared online space (larger online storage plans available for purchase) Unlimited local storage Limited to 50,000 citations and 2 GB of attachment storage 2GB of cloud storage
Attach associated files (PDFs, etc.) Yes, with option to attach automatically Yes, and can highlight and annotate PDFs Yes, and can highlight and annotate PDFs Yes Yes, and can highlight and annotate PDFs
Search full text of PDFs Yes Yes Yes No Yes
Create group or shared libraries Yes Yes, free for up to 3 group members (larger group plans available for purchase) Yes, with EndNote basic account Yes Yes
Create bibliography with different styles Yes Yes Yes Yes Yes
Automatic citation extraction from PDFs Yes Yes Yes No Yes
Other features Sync library with multiple computers
Use tags to organize/search
Sync library with multiple computers
Sync with Zotero library
Insert figures and charts using word processor integration  

Use tags to organize/search
Export references as an RIS or BibTeX file

Last updated February, 2016

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