Why I Settled on Mendeley for Organizing Research

MendeleyLogoWe have posted a few times about solutions for organizing dissertation research and references.  (Evan has shared his experience with DEVONthinkPro Office and Kim has offered a comparison between Zotero and Evernote).  I have recently started to revisit some of the research I’ve collected over the last few years in preparation for the doctoral comprehensive exams, and have realized what a lifesaver Mendeley has been.  Back in 2008, I had files across multiple locations and devices — some on a laptop, some on a desktop, some on a collection of flash drives.  I hadn’t gotten the hang of this new thing called cloud-based storage.  But then I found Mendeley, and my virtual research space has been much tidier ever since.

What’s So Good About Mendeley?

Here's an example of what my Mendeley desktop looks like when reading a file.

Here’s an example of what my Mendeley desktop looks like — here I’m searching a PDF.

Mendeley, like RefWorks and Zotero, is essentially a reference manager for organizing sources. However, unlike RefWorks and Zotero, Mendeley has a social networking component that allows users to potentially find akin researchers and share research libraries.  Mendeley is free (there is a fee for storing more than 2 GB of research) and works across multiple operating systems.  I work on multiple machines, both Macs and PCs, so the ability to switch between operating systems has been a great help.

Mendeley has both a web based application, but also requires a destop download.  The local and web based files sync upon signing in, in the same way Dropbox works.   Like RefWorks and Zotero, Mendeley includes a citation manager and exporter.  Mendeley supports 4311 citation styles (who knew there were so many), but I’ve been using APA.  Despite each of these helpful features, what has been the greatest asset in helping me to stay on track is Mendeley’s impressive PDF reader and organizer.

Managing PDFs with Mendeley

Mendeley allows users to upload PDFs for storage.  (Note that users can include reference entries for other types of sources, like books or films, however Mendeley storage is limited to PDF files).  What I love most about the system is the ability to conduct a title or keyword as well as a full-text search of the stored pdfs.  In the screenshot above, I searched my Mendeley files for the term “digital divide” and came up with a number of hits.  Then, I opened a few of the articles within Mendeley, and search the same term within the full text.  Mendeley finds each instance of the search term, and allows me to quickly click through each instance.  Additionally, Mendeley makes it easy to have several PDFs open at once, and to easily move between them by clicking through the tabs.

This is what it looks like when I comment on a PDF in Mendeley.

This is what it looks like when I comment on a PDF in Mendeley.

In addition to the search tool, Mendeley also includes a highlighter, notes areas, and other annotation tools.  I’ve been using the general notes area text box to jot down thoughts and page numbers for sources that would not import as PDFs, like books.  Since most of my research is available in PDFs, though, the Insert Note annotation feature has been more beneficial in helping me navigate back through an article.  (The highlighter could be a great tool for collaborative critical reading.  You can read more about Mendeley for supporting collaboration here in Sharon’s post).

Social Nature of the Web Interface

Here's a list of crowd-sourced popular papers.

Here’s a list of crowd-sourced popular papers — sometimes you can find helpful articles from other users this way.

One of the alluring aspects of Mendeley for many folks is the social nature of its Web interface.  Like Facebook or LinkedIn, Mendeley encourages users to make contacts.  Your contacts can post onto your Mendeley wall.  You can also establish research groups and shared group collections.  You do have the option to keep your research collections public or private.  I initially chose to keep mine private.  However, in order to share my research with my doctoral advisor, I eventually created a public “group” for my research collection.  This means that other Mendeley users can request permission from me to become a member of the group in order to see and share references.

One other feature of the social Web version of Mendeley that others might find interesting is the ability to search Mendeley’s crowd-sourced catalog of references.  While I certainly would never recommend that folks use Mendeley’s search tool in place of database searches from Swem, I have to admit that I have on occasion found journal articles in Mendeley with high readership that I otherwise would have ignored.

Mendeley’s Citation Manager

Mendeley includes a citation manager, and for me it has worked OK.  Prior to Mendeley, I tried RefWorks for a little while.  One thing that both have in common is that the outputted citation is only as good as the inputted bibliographic information.  Neither, in my opinion, work as an “automated” citation generator.  That said, Mendeley does allow you to export your citations.  This requires a simple plugin installation in Word.

Mendeley Has Improved my Productivity, But There Are a Few Caveats

I’m pretty sure that the Mendeley PDF organizer and it’s related tools have improved my productivity and organization.  But it’s not perfect.  Sometimes the bibliographic information does not translate correctly during import.  At the end of the day, it takes a human to check the citations and the reference entries.  One annoying deficiency in the organizational structure of Mendeley is its inability to nest folders.  While you can create as many folders as you like, you still cannot create folders within folders.

In addition to that, the PDF-only storage system would make this platform quite limiting to folks who need to also organize images, audio, or multimedia files.  It may be no wonder, then, that Mendeley seems to be used more often in the sciences and social sciences than in the humanities.  Despite these limitations, Mendeley seems to be a robust and user-friendly reference manager.  (If you’ve read this far down the page, you might be interested in taking a look at Mendeley’s comparison chart with other reference managers).

If you have already established a working system for collecting and organizing research, I’m not sure Mendeley is compelling enough for you to rethink your system.  (Use what works best for you).  After some trial and error I found that Mendeley is what works best for me.  If you’ve used Mendeley, please chime in and let us know what you think.

About April Lawrence

April Lawrence is the Academic Technologist for the School of Education. A high school English teacher for ten years, April also worked in online course design and development before joining the AIS staff. April is a doctoral candidate in Educational Policy, Planning & Leadership at William & Mary. Her research interests include exploring the intersections of culture, technology integration, and learning.


  1. Hey April, thanks for the post. Just dropping in here to confirm you’re right about the OCR – it isn’t done natively yet, but we do hope to implement that at some point. Also, it’s kinda hidden, but you can attach other kinds of media to your documents. At the bottom of the details pane for an item, there’s a place where it says “Files:” and you can click in the box below that to add any kind of media – images, video, audio, spreadsheets, presentations, etc.

    Hope that helps!

    • That’s great news- I’ll look for place to add media files. Thanks for the update, and thanks for reading our blog!

  2. Milton Lee says:

    Hey, nice write up. I’m a big Mendeley fan and it’s saved me a heap of time. Just had to point out – you are dead wrong re nested folders. Just click and drag one folder to nest it under another.

    I also like the way Mendeley detects PDFs which have imported improperly, and adds them to a “needs review” folder.

    It would be interesting to hear your thoughts on mendeley vs endnote for 1) long term use and 2) use for a specific short term project.

    • Hi Milton- thanks! You are correct- I just tested dragging folders in the Mendeley desktop, and I can now get nested folders. The ability to have subfolders is a great improvement. I did notice that subfolders are not yet available in my web app library, but I spend more of my time in the desktop application. Thanks for pointing this out, Milton!

  3. Hi April — thanks for this overview of Mendeley; I think I might check it out for some aspects of my own research. I have a question for you: You mentioned that the text of the PDFs put into Mendeley are searchable. Does this work for PDFs that aren’t OCR-ed, i.e. do you know if Mendeley automatically OCRs documents that you put into your account?

    • Hi Kim- thanks. No, Mendeley does not yet have OCR conversion built in natively. (It is a recommendation currently under review according to their customer feedback page). You could use a third party for OCR conversion (like Adobe Acrobat Pro or the free and clunky conversion tool in Google Docs), although that may add a cumbersome and unwelcome step in your research flow. Most of the PDFs I’ve added have been searchable, but I haven’t added anything I’ve scanned myself.