Using Mendeley to Manage Readings and Citations

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It seems that half of the battle in a PhD program is not doing the work, but knowing how to accomplish it. Sure, I can read through five journal article PDFs for a class, but what’s the best way of going about reading/annotating/synthesizing and coming up with discussion points for class? I found myself asking this question early on in the semester and was quickly pointed to Mendeley by a couple of my fellow CRDMers. And how quickly I’ve come to appreciate this cool platform for how well it manages my readings! I thought I would share how I use Mendeley, because if there are other graduate students out there like me, sometimes you just don’t know these programs are out there to use, and they sure make your life a lot easier once you find them. I know that I’m also not using Mendeley to its fullest advantage, so if there’s another neat function that I don’t mention, please point me to it.

I use Mendeley to read journal article PDFs, to annotate readings for class, and to organize all of the files and notes that I accumulate throughout the semester. I’ve downloaded the desktop software application, which serves as a database for all of the files. When I have a new reading for a week, I save the PDF on my computer and then upload it into Mendeley. When I open the file in Mendeley, I can highlight lines in the reading, insert notes in the margins that look like Post-It notes, and search the text for key terms. My favorite features is probably the Post-Its: the graphic for it is really cool, and they appear both in the side bar with my notes and in a little bubble in the PDF to show me where I’ve inserted them.

Sample file in Mendeley desktop with Post-It notes

I can also use Mendeley to manage my research sources as I continue to work on my seminar projects. It will generate a bibliography for me from the bibliographic information of the PDFs, saving me much time down the road. (Although, I must admit, that I like doing my bib by manually entering the citations, as inefficient as that is!)

Something I wish I could change about Mendeley is the default opening screen: it opens to an  “All Documents” folder, which lists all of my PDFs. To me, seeing all these files is overwhelming; I’d like to archive them in files like you can with your Inbox so that only my current readings are displayed. You can currently label PDFs so that they appear in a certain folder, but they continue to appear in “All Documents.” Anyone know if this is possible to change? Or am I stuck with it like this?

The Mendeley website also has capabilities for sharing sources with others who are researching similar topics or who want to swap readings. I also found out via a Twitter user that I can use the website to upload PDFs of my students’ essays that I’ve graded by inserting Post-It comments and share them with their respective authors – something I’m definitely open to trying. Ideally, I’d be able to export the file from the Mendeley desktop and email it back to them, but I’ve been told that is not yet possible. (Note to the Mendeley people: can you make this happen? Signed, an Appreciative Instructor.) There’s also a social component to the Mendeley site where you can search other Mendeley users to see what other people are reading and researching. Overall, this is a must-have tool for graduate students and academics.

So – what am I missing? How else can I use this software to expedite my research process? Tell me more!

7 thoughts on “Using Mendeley to Manage Readings and Citations

  1. > Anyone know if this is possible to change?
    > Or am I stuck with it like this?

    The ‘Unsorted’ folder displays documents which have not been added to any other folder, so you can use it like an Inbox. You can also use ‘Recently Added’ to see quickly see recently added papers.

    We have discussed other options such as a ‘Recently Read’ list and so on for future releases.

    > Ideally, I’d be able to export the file
    > from the Mendeley desktop and email it back
    > to them, but I’ve been told that is not yet
    > possible.

    You can export a PDF with annotations when viewing a PDF using File -> Export PDF with Annotations.

    — Rob Knight (Mendeley Desktop developer)

  2. I still wish Mendeley had been available when I started my PhD. Instead I did most everything using OneNote. However I believe you are definitely on the right track here.

    If you haven’t read it yet, please read Demystifying Dissertation Writing. I wrote a review on my blog ( of the first 5 chapters, which talk a LOT about how to take notes and organize your research. Those chapters also talk about choosing your advisor and topic; some of the best advice I got (and managed to ignore) was to pick a general area or topic early use it as a topic for all your in-class papers and research work. It will give you a leg up on being an “expert” by the time you get to writing your dissertation!

  3. Rob – Thank you for the information! I think having the home screen as unsorted/currently working on files is more helpful than the entire library. I’m also glad to hear I can export PDFs and share with my students!

    Protoscholar – I’ve read through some of your posts and have found them quite helpful and informative! (Especially the ten productive writing tips.) You are now added to my Google Reader, and I look forward to future posts. 🙂

  4. Hi Meagan, Not sure where you are in the process of your own PhD, but I’ve found Mendeley invaluable to organizing vast amounts of information. I’m finalizing my proposal and used the notes feature in Mendeley to find quotes to construct my lit review. I also like having all my notes backed up online. Great tool and great post!

  5. Cool. I didn’t know you could annotate and highlight with Mendeley. I’m in an office and have the habit of printing everything out. The environment hates me.

  6. Hey Meagan,

    What an awesome resource! Thanks for sharing. I use Diigo for organizing and saving websites, but it doesn’t do too much for reading and research. I am not doing as much research as I was, but I am teaching, and this will be invaluable to me as I collect articles for my students to read.

    I hope all is going well for you!


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