Guides: Biology: Citation Management Tools

About citation managers

A citation manager helps you keep track of articles and books as you find them, tag and annotate them, and easily create citations and bibliographies in Microsoft Word, Google Docs, or other writing software. Using any citation manager will be more efficient for most scholars than not using one at all.

Most citation managers consist of three parts:

a collection of your citations,
browser plug-ins to more easily capture citation information from your sources,
a plug-in or other way to easily get your citations into your work, usually in a variety of citation styles.

Even if you use a citation manager, you will still need to consider what citation style you plan to use (even though the formatting with many citation managers is automatic). This guide also include information about citation styles.

In this guide, you'll find information on: RefWorks, Zotero, Mendeley, Endnote, NoodleTools, and PowerNotes.

If you have questions about choosing a citation manager, contact a librarian. You can contact your subject librarian for guidance. Also, feel free to contact us to when you have questions about best practices or if have trouble with these tools.

Citation Managers

RefWorks is provided by Penn Libraries for the Penn community (including alumni). It is a well-established platform, but has limitations in terms of working with PDF files.
Endnote works well for the health sciences and for large collections of articles, despite some technical and installation issues.
Zotero is an open-source software program that is easy to use. It has screenshot and simple web archiving capabilities.
Mendeley is research management software, so it includes search and PDF annotation. It suffers from accuracy issues.

Full Comparison of Citation Software

Thanks to Mat Willmott at MIT Libraries for creating the template for this chart.

	RefWorks	Zotero	Mendeley	EndNote
Link to web guides	Proquest guides and videos	Documentation	Support	Support
Type	Web-based	Desktop software and browser add-on for Firefox, Chrome, and Safari (newest version includes single sign-on through zotero.org)	Desktop software and web-based. Works with IE, Firefox, Chrome and Safari	Desktop client sofware. Also web interface, EndNote Online
Cost	Free via Penn license. Sign up for an individual account on the RefWorks website. (Penn only)	Free with Penn license with additional storage. Download Zotero	Free with 2GB of web space and 100 MB shared library space. Storage upgrades available for a monthly fee. Download Mendeley	Access to EndNote is free via Penn Library site license. Access Guide with download link.
Learning curve	Fairly quick to learn; many online user guides and demos	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 training
Strengths?	Allows users to share citations Good for organizing citations for papers Web-based Since Penn has a site license, there's no cost Available to Penn alumni as long as Penn maintains its subscription	Simple download of records Good for managing a variety of formats, including webpages Offers most functionality in a free, open-source product Useable PDF reader Downloads records from with several databases that don't work with EndNote and RefWorks, such as Factiva and USPTO	Great for managing PDFs Has a social aspect. Can see what other users are reading and citing. Does an excellent job of pulling citation metadata from PDFs Can share citations and documents with others	Excellent for organizing citations for papers and theses Best option for major research projects, because it offers the most options for customization and formatting Most output styles for formatting Most customizable Can handle a large amount of references
How does it work?	You export references from compatible databases into RefWorks	Zotero can tell when you are looking at an item and shows an icon for it in the Firefox URL bar. Click the icon to add the item to your Zotero references	You export references from compatible databases. Retrieve metadata from pdfs that you uploaded directly from your hard drive.	You export references from compatible databases into EndNote
Does it have many output styles and bibliographic formats?	Yes, many popular styles and formats	Yes, many popular styles and formats	Yes, many popular styles and formats	Yes, many popular styles and formats
How simple is it to import records?	Simple to import records from most research databases Always check the citations against the article itself	Very simple, as long as the resource is compatible with Zotero, but you will want to verify that the records are complete after import Always check the citations against the article itself	Very simple using the Mendeley browser plugin. However, the import doesn't work with as many databases as other products. Always check the citations against the article itself	Simple to import records from most research databases Always check the citations against the article itself
What kinds of records can you import and organize (PDFs, images, etc.)?	Records for articles and books	Books, articles, patents, and webpages; Can also store PDFs, web screenshots, files, and images in records. You can make PDFs searchable by choosing to index them in the preferences menu.	You can import bibliographic citations, web pages, and PDFs. You can also manually add citations	Can organize records for articles and books; PDFs and other file types can also be stored in the records. Can download PDFs in batches.
Are records in your library viewable by others?	Yes; Users can share references in library with other RefWorks users	Yes. Users can set up individual and group profiles and share records	Yes. Users can set up private groups to share references. Users can decide whether or not to make their library viewable by others	Yes, but you must create and sync your desktop library with an EndNote Online account.
Can you export records to other citation software?	Yes	Yes	Yes. Export to EndNote XML, RIS and BibTeX	Yes
Is managing and maintaining a big library (1000 records) complicated?	Not complex, but it can be cumbersome to manage large libraries	More difficult; takes time to sort out duplicates and verify that records are complete	No known problems. May need to purchase extra space.	Not complex; EndNote is best option for maintaining large libraries
Does it work with word processing software? You may need to get assistance from your school IT to integrate with Word	Works with Word and Google Docs through RefWorks Citation Manager add-on or (for older versions of Word) "Write-N-Cite" feature, with LaTex through BibTex,	Works with Word and Open Office; also works with LaTex through BibTex. You can create a list of Works Cited for Google Docs	Works with Word and OpenOffice.	Clean integration with Word and powerful formatting and customization features; also works with Open Office and LaTex through BibTex
Does it back up your records?	Yes	Yes, if you choose to back up or sync your Zotero library. A small amount of storage is free.	Yes	Not automatic. Backing up an EndNote Client Library is a manual process. If you create an EndNote Online account and sync your library then it's backed up in cloud. You should periodically, manually, backup your desktop client library.
Other important features	Since it's web-based, you're not limited to a single machine	If you back up records, you can sync multiple computers Integrated with Zotero web library Fastest download of records Saves snapshot of web pages Allows users to highlight text and take notes on page Allows users to tag records	Has a good PDF reader that enables highlighting and comments	PDF file management and organization features

Biology: Citation Management Tools

About citation managers

Most citation managers consist of three parts:

Citation Managers

Full Comparison of Citation Software

Link to web guides

Type

Cost

Learning curve

Strengths?

How does it work?

Does it have many output styles and bibliographic formats?

How simple is it to import records?

What kinds of records can you import and organize (PDFs, images, etc.)?

Are records in your library viewable by others?

Can you export records to other citation software?

Is managing and maintaining a big library (1000 records) complicated?

Does it work with word processing software?

Does it back up your records?

Other important features