Reference management tools

reference manager workflowReference Management Tools help scholars to create and manage their lists of references for research projects. Most tools are designed to organize citations into specific formats for the preparation of manuscripts and bibliographies. Many search tools provide ways to download references into reference management tools. There is a wide variety of reference management software, and the strengths and weaknesses of reference management software are perceived differently depending on the workflows of different disciplines or individuals. Some reference managers allow the sharing, collaborative editing, and synchronization of reference databases across a private workgroup and/or publicly via the internet.

Building a reference list is not the cumbersome chore it once was. Reference management systems enable you to save, store and manage your bibliographies while you’re searching for information across databases and web based resources. A reference management tool can also insert in-text citations as you write up your research, thus automatically building your reference lists. Use these time saving tools as personal libraries and even as sites of collaboration with other researchers. In this week’s post we look at four particular tools:


EndNote is a desktop program that allows you to store, file and search bibliographic references, PDFs and images. It has a unique ‘Cite While You Write’ functionality that inserts citations and bibliographies into your written work. It is  free to students and staff of the Charles Sturt University for both PC and Mac.  Most academic institutions provide access to students, so check with your own organisation before purchasing this product.

Your EndNote Library is a fully searchable database that you can annotate with research notes, which is great for literature reviews. You can link PDFs of articles to the relevant EndNote reference and also annotate these PDFs stored in your library. One of EndNote’s major strengths is its stability; it rarely fails. It has a cloud based back-up system in Endnote Online.

EndNote Online can be used to collect, manage and view references from any computer. An EndNote Online library can also be synced with the Desktop version on multiple computers and with the EndNote iPad app. Share part, or all of a library with colleagues. Sharing full-text content with others may breach copyright or license conditions so check these details carefully.

Endnote X7 imports PDFs and citation information directly from a folder on your desktop: great when you are finding articles through social media or other ‘non-traditional’ sources.

Well established: it’s up to version X8. Steep learning curve – but once learnt and set up for your purposes can be very easy to use.
Wide user-base in the academic community: more opportunity for peer support. Limited portability and sharing: EndNote is also now as a web-based version (EndNote Online).
Well supported
Customisation: an expansive range of editing output styles, document types.


Zotero logo.

Zotero [zoh-TAIR-oh] is a free open source program to help you collect, organize, cite, and share your research sources. You can attach PDFs and other files to references in your library and insert citations into Word, Google Docs and Open Office. References can be tagged and sorted to allow advanced searching.

Versions of Zotero

  • Zotero for Firefox is a browser extension enabling you to capture and organise references without leaving Firefox. A plugin is needed to insert citations into Word documents.
  • Other platforms
  • Plugins – Install one of the many third-party plugins and become even more productive. Browse Plugins
  • Zotero Standalone is a separate program downloaded to your computer and can integrate with Firefox, Chrome or Safari. Word plugins are included.
  • Zotero Connector automatically senses content as you browse the web and allows you to save it to Zotero with a single click. Zotero Connector for Firefox.   Zotero Connectors for other browsers
  • See Zotero: Useful resources

An advantage of Zotero is that you can export lists of articles (and PDFs) or books from many major databases and websites with just a few clicks. It’s also useful for exporting references from less traditional resources like websites and wikis. You can also set up a Zotero web account to sync your library from any location.

Tight browser integration. Only works with Firefox, Chrome and Safari.
Free, open source, and actively developed. Cannot automatically format citations in Author (Year) style.
Functionality can be extended with add-ons.


Mendeley Mendeley is a free reference manager and academic social network. Make your own fully-searchable library in seconds, cite as you write, and read and annotate your PDFs on any device. Mendeley is a free application comprising two components – Mendeley Web and Mendeley Desktop – that allow you to generate citations and bibliographies in Microsoft Word, OpenOffice and LaTex.

Anotate as you read – Easily add your thoughts on documents in your own library, even from mobile devices. For ease of collaboration, you can also share documents with groups of colleagues and annotate them together.

You can add and organise PDFs in your library from your computer, as well as import PDFs from other reference management tools such as EndNote, Papers or Zotero. PDFs can be read and annotated using sticky notes and highlighting tools. Import papers and other documents from your desktop, your existing libraries or websites with ease. Mendeley automatically captures information like authors, title and publisher, which makes organization and browsing easy.

Mendeley’s strength lies in its networking and collaboration functionality. Researchers can collaborate securely online to share papers, notes and annotations with peers and can network and discover papers, people and public groups. Users can form groups that can be either public or private. Public groups are open for new members to join and share resources and communicate with each other.

As with most contemporary reference tools, Mendeley can sync your library via the web, iPhone or iPad.

There are many more videos available on YouTube:

Free (2 GB storage). PDF specific.
Extensive social networking features. Strong science community presence, but not humanities.
Crowd-sourced research catalogue of over 100 million papers. Syncing between desktop app and Mendeley web can be slow.
Easy to edit citations in Word. Beware copyright issues when sharing copyrighted PDFs.
Can access Mendeley library across various platforms.


If you like to use Google Docs for writing papers & need a citation management tool that works with it, you have some options.  One is to follow the directions in this guide from Princeton University,which shows how to use EndNote, Mendeley, Papers 2.0, and  Zotero with Google Docs (there is no integration, but there are workarounds that you can use).

Another option is to use an add-on for Google Docs, Paperpile.

In Google Docs, from the Add-ons dropdown menu, select Get Add-ons, & search for Paperpile (you can also search for citation management to find other add-ons).  With Paperpile, you can search for literature as you’re writing, then add citations as necessary.  Even better, if you do use another citation management tool, you can export these citations to that program.

  • Keeping a library with thousands of papers organized can be daunting. With Paperpile it’s easy (and fun).
  • Add hierarchy to your library with folders. Put every paper in the right folder to quickly find it again.
  • Group papers visually with colored labels and use them as powerful filters.
  • Search even large libraries with tens of thousands of papers instantaneously.
  • Search for keywords, authors, journal or publication year and find a paper quickly when you need it.

Try this

  • If you have a Zotero account:
    • Share your own work or sources you have discovered with others who are working in related areas.
    • Collaborate with colleagues, publicly or privately, on ongoing research.
    • Discover other people with similar interests and the sources they are citing.Set up a Zotero group – either public (open to all) or private (invite only) – to share your references with others. With groups, you can collaborate remotely with project members, set up web-based bibliographies for classes you teach, and so much more.
  • Read Tips and Tricks for searching tags and organizing your hard drive files in Mendeley

Explore further

  • Comparison of other reference management tools.
  • Best reference management software for students and research-oriented professionals.
  • How to choose a citation manager.
  • Explore other reference management tools:
    • CiteULike – a social networking tool for discovering and managing references.
    • JabRef – a freely available BibTeX citation management tool suitable for LaTeX documents.
    • Papers – collaborative citation management software, allowing you to organise, discover, and cite research.
    • Sente 6 – a free academic reference management app for Macs and iPads that allows you to sync your library between devices.
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