Skip to main content

NREM: Natural Resources Ecology and Management Research Guide

Research guide for the NREM department and affiliated programs of study – animal ecology, forestry, fisheries, land management, etc. - recommended databases, search tips, and more.

Citation management tools

Bibliographic or citation management tools can take a lot of the work out of organizing and using references. They do this by collecting, organizing, and storing the citation information about the references you save, and integrating that information into a word processor to automatically generate citations and reference lists for you.

If you are already using a citation manager or would like help getting up and running with one, ISU librarians provide support for three options: EndNote (paid and free / basic), Mendeley (free), and Zotero (free).

The sections below provide links to ISU Library guides for each citation manager and some basic information about their strengths and weaknesses.

Which citation manager?

There is no one citation management software that is objectively "better" than another. All of the citation managers listed here share the same basic functionality: storing and organizing bibliographic information, generating citations, integrating with web browsers and word processing software, and allowing for collaborations / group projects.

You will need to choose the option that makes the most sense for you. If you are collaborating with others and they are already using a citation management program, it would be a good choice to use the same system.

The Library supports EndNote Basic (formerly called EndNote Web), Mendeley, and Zotero.

Compare your options: Here's a good list that compares EndNote, Mendeley, and Zotero, created and maintained by librarians at Penn State University Libraries.

Regardless of what you choose, don't expect the software to be perfect. You will almost certainly need to clean up some of your citations or do some tweaking at some point.

EndNote Basic

EndNote has the greatest functionality (probably more than most researchers would ever need to use), but you have to buy the software. See TechCYte for information on available versions and pricing.

EndNote Basic is cloud-based and totally free online. ISU affiliates have access to many citation styles and tons of storage - again, more than most researchers would ever need. You can also share references with collaborators. If you have both EndNote and EndNote Basic, you can sync them together. However, there is no need to have or use both - they are independent of each other.

If you frequently use Web of Science, consider using EndNote or EndNote Basic. Since Web of Science and EndNote are owned by the same company, they integrate seamlessly.

We regularly hold workshops for EndNote Web.


Mendeley also has both a desktop version and a cloud-based version. Unlike EndNote, Mendeley's desktop version is free and must be downloaded onto your computer. The cloud-based version of Mendeley is also free.

Mendeley's desktop version has the greater functionality, while its cloud-based version provides some social network features. You can sync your records also. Unlike EndNote, there is a greater need to use both Mendeley's desktop version and its cloud-based version together.

For many people, a major pro of using Mendeley is that you can drag and drop all those PDFs you've been saving into the desktop version, and it'll do its best to pull out metadata and turn those PDFs into usable citations. (Note: you will probably have to do at least some cleanup, but it's often better than tracking all the articles down again to use the web plugin or trying to add dozens or hundreds of citations manually.) It also lets you annotate and highlight the PDFs right from Mendeley.

If you are an ardent collector of PDFs, or if you want to use your citation manager to track down papers related to your research, consider using Mendeley.

We occasionally hold workshops for Mendeley. If there are no upcoming workshops, contact the librarian listed on the Mendeley guide for assistance.


Unlike Mendeley and EndNote, Zotero is an open-source citation management program. Zotero exists as a desktop application, which connects seamlessly with Word, and a "connector" for each of the major browsers that allows you to gather citation information from the web. Zotero also does a fairly good job of pulling metadata (citation information) out of PDFs for you.

Zotero integrates very well into the most commonly used browsers for Windows, Mac, and Linux. It can collect better, more complete citations than the other options in some cases, especially from web resources. The latest versions of Zotero utilize Unpaywall to find free PDFs of articles and connect with Retraction Watch to flag retracted items. Like EndNote Basic and Mendeley, it can be seamlessly integrated into Word and other word processing programs such as LibreOffice. You can also use Zotero with Google Docs in Firefox and Chrome!

If you are interested in open source alternatives to the mainstream citation management programs, or are interested in a citation manager that works with Google Docs or can help you find free (and legal) versions of papers, consider using Zotero.

We occasionally hold workshops for Zotero. If there are no upcoming workshops, contact the librarian listed on the Zotero guide for assistance.

Megan O'Donnell's picture
Megan O'Donnell
150 Parks Library