How I use Mendeley to organize my papers

Since starting my graduate studies, I’ve experimented with several different systems for organizing my research papers, both electronic and paper-based. Eventually, I settled on a comprehensive system that works well for me, that’s based on a combination of my personal cloud server and the reference manager Mendeley.

The main advantages of my system are:

  1. It’s free (I personally pay for extra storage on my drive, but the free storage provided by most cloud servers is definitely sufficient if you’re only storing papers).
  2. It synchronizes between all of my devices (I can view my papers and annotations on my MacBook, my Windows PC in the lab, my iPhone and various other devices that I won’t mention for the fear of sounding like a fat-cat)
  3. It’s fast (It doesn’t interrupt my normal stream of browsing)
  4. It’s neat-freak friendly (folders and subfolders are the essence of life)

The initial set up

I installed the Mendeley Desktop app on my MacBook and on my PC in the lab, and the iOS Mendeley app on my iPhone.

By default, Mendeley stores all of your library documents on the Mendeley server, which provides 2 GB of free storage (equivalent to approximately 700-800 articles). While this may seem like plenty if you’re just opening an account now, trust me when I say that it isn’t, especially once you develop a steady habit of adding papers to your library.

The good news is that Mendeley lets you choose your own storage location for your documents, which means that you can surpass the storage limit without having to pay > $50 a year for a premium account.

I chose to copy my papers to my iCloud, but this could be any other server (Google Drive, Dropbox etc.). You could also choose to store your files in a local directory, but that would be a bit silly since you’d miss out on advantage no. 2 of the system.

To set the storage location, go to Preferences File Organizer → tick the “Organize” checkbox, and set the directory to a location on your drive.

Another advantage of having Mendeley copy my library documents to my iCloud (other than the increased storage) is that I can access them from any app that has access to my iCloud folders (e.g. alternative reading apps like Kindle or annotation apps like Markup).

Another feature which is especially appealing to Type A personalities like myself, is that Mendeley can use a consistent naming scheme within the storage folder. Under “File Organizer” you can also check the “Sort files in subfolders” and the “Rename document files” checkboxes. I chose ‘Author’ for subfolders and ‘Author-Year-Title’ as the scheme for my filenames. For me, the author name followed by the year of publication seems to be the best match for the hierarchy in my brain, but you could choose whichever combination suits your own mind best.

Adding new papers during a literature search/browse

I add new papers to my library in one of two ways:

(1) Through the Mendeley web importer:

You can download a browser extension from the Mendeley webpage which lets you save papers from major literature databases like PubMed, Google Scholar, IEEE Xplore and PLoS. The extension works on most major web browsers, including Safari, chrome, Firefox and Internet explorer (but let’s be honest, if you’re using the latter you really don’t deserve a PhD title).

The web importer allows you to add a paper (and download the PDF, if it’s available) to your library with a single click. It also lets you edit the details of the publication and select the destination folder in your library (so there’s no need to do any further organization later on). I don’t always use the web importer to sort my papers, but more on that in the next section.

The web importer is the main tool I use to add new papers to my library. I typically find papers by searching PubMed or Google Scholar on a computer with access to multiple journals, so it’s simply a matter of clicking ‘Add to Mendeley’.

(2) By dropping PDFs in the ‘Watched folder’

On the off chance that I don’t have access to a certain paper online, but I do have the PDF (e.g. a black raven with a red key in its mouth mysteriously dropped it my downloads folder), I can place it in my Mendeley ‘Watched folder’. This is a directory that Mendeley monitors, who’s contents are automatically pulled into your library. You can set the location under PreferencesWatched folders. Files dropped here will appear in the ‘Unsorted’ folder in your Mendeley library.

Organizing papers

Organization is a very intimate topic, but nevertheless the title of this post is how use Mendeley. As I already mentioned in the beginning, two of my greatest passions in life are folders and subfolders, so needless to say these are the backbone of my Mendeley library*.

*As I explained in the ‘Initial set up’ section, the original files (stored on my iCloud) are saved in folders and subfolders named after the author and year of publication. That’s what I see when I manually navigate to a file on my iCloud. However, what I look at 99% of the time is the library on the Mendeley app, and that’s the one I make an effort to organize.

I sort my Mendeley library by scientific topics. Naturally, major subjects of interest to me get folders, and topics within that field get subfolders. I don’t waste my time by creating copious amounts of subfolders for every single subject that I’m interested in, but I have found that it’s worthwhile to invest in making lots of subdivisions for important topics. For example, the folder dedicated to my main PhD subject (the neural extracellular matrix) has lots and lots of children. This has come in handy on multiple occasions, and I’m sure it will ultimately expedite my thesis writing.

Mendeley has several additional organizational features, for example you can ‘favorite’ papers, mark papers for future review and add searchable tags.

Personally, I don’t use any of these features. My workflow is fairly simple: once I come across a new paper that I want to save, if I feel that I’ve read enough and only want store the reference, I’ll add it to the relevant topic folder/subfolder (either directly through the web importer or by dragging it from the Unsorted folder in Mendeley). However, if I want to read more (or all) of the paper, I won’t sort it just yet. So my Unsorted folder is effectively my ‘to read’ folder. And once I’m done reading, I’ll catalogue the paper by topic.

It stands to reason that my Unsorted folder is very rarely empty. But in the words of John Steinbeck: “I guess there are never enough books.”

Reading and annotating papers

I find the Mendeley app to be more than sufficient for both reading and annotating papers. Once you double-click a paper in your library, it opens in the Mendeley annotator. Like most basic PDF annotators, you can comment, make notes, highlight (with multiple colours 😀 ) and export your annotations.

One feature that I particularly like is that you can write a ‘general note’ on a paper in your library. I use this feature to summarize important points from the paper in my own words (only for important papers and only if I have time, I definitely don’t do this for every paper in my library), or general notes which might come in handy in the future.

If you feel like you’re in need of some more advanced features, or you already have a favorite reader/annotator, that’s where the personal cloud storage comes in handy. You can open the files on any app that can access your cloud and use Mendeley solely for organization.

Citing papers

If you write with MS Word, you can install the Word plugin (through the Tools menu in the app). This allows you to add citations from your library directly into your Word document (in any citation format you choose), and to automatically populate a bibliography at the end.

I recently started writing with LaTeX, so I use BibTeX to cite. Mendeley can automatically generate a bibtex library with the keys Firstname<year> (e.g. Dankovich2015 …not mine, unfortunately). Since I assume this may not be relevant to the majority of the readers, I won’t go into the technical details of how to integrate BibTeX and Mendeley, but here’s a link to the HowTo.

A neat citing feature in the Mendeley app (that I use quite often) is citations/bibliographies on the fly. If you select one or multiple papers in Mendeley and press Ctrl-C (Command-C for Mac), you can Ctrl-V (Command-V) those guys wherever you want, and get a quick list of citations.

I hope these tips were useful, or at least gave you an excuse to procrastinate a little by moving papers around instead of reading them.

I’d be happy to hear your own tips and tricks for organizing papers.

Tal Dankovich

PhD candidate, Neuroscience, University Medical Center Göttingen (UMG)

This Post Has 4 Comments

  1. Yaroslav

    Thanks for sharing your approach, it’s helpful to people like me who just started to work with Mendeley.

  2. Chris Tennant

    This is great. But how do you tell Mendeley to copy files to a folder in iCloud?

  3. Antti Mäki

    nice post.
    I just wonder, have you considered to use tags (see e.g. Tags and filtering section in

    If not, I highly recommend to check, might help you on your studies. Pretty easy to organize papers without making folders and subfolders (no need to move single document to multiple Mendeley folders).

    For BibTeX, you can filter your tags to choose just documents that are with certain tag(s), and export those as .bib file or “copy as bib format” to be pasted in your own .bib file.
    (latter option I use e.g. if I want to add some new references to existing .bib file)

Leave a Reply