6 April 2010 by Ricardo

As a PhD student I find myself roaming the Internet quite a bit in search of literature for my research project which can be really time consuming. Looking for the right keywords, opening each relevant result into a new tab, downloading each paper of interest, finding the cryptically named PDF file and then adding it to your library in an organized fashion (phew). So anything that can cut back this strain of accessing and organizing research papers is most welcome.

In previous posts I’ve mentioned Mendeley’s web importer, which helps retrieve papers directly to your Mendeley Web account. That’s all good, but what about papers that you already have on your computer spread about in different folders or hard drives?

There are multiple ways to import files from your hard drive directly into Mendeley Desktop. You can add one file at a time, a full folder in one go or even make a specific “Watched” folder.

A “Watched” folder is basically a folder that Mendeley keeps an eye on for any new files and automatically imports new documents with minimal interaction on your behalf. Just drop or download your PDF documents into your watched folder and Mendeley will do it’s thing (I mean auto-extract it’s metadata and add it to your library!).

So we now have a web importer for online retrieval and an automated watch folder. Looks like we are set!

My references and documents are all nice and organized within Mendeley Desktop and accessible online but when I look at the files on my computer, I notice something. In fact, I notice the lack of something: meaningful file names.

Filename Mystery

As you can see in the image above, the file names are not very explanatory and whenever I have to pick a file to send to a colleague or open it directly for some reason, it becomes a guess-the-mystery-file name game. Not to mention that every time I add a file to that folder with a similar name, I get this fantastic message:

The file you are trying to copy “sdarticle.pdf” already exists. Cancel or overwrite?

Good question, do I want to overwrite sdarticle.pdf? Do I have any idea what is in that file? The most probable answer to both these questions is no. Once again, Mendeley has considered this situation and provides an effortless way to organize your files with a built-in feature called: ‘File Organizer’.

As the name suggests, this feature can organize your files for you in a few different ways. You can store your files in a centralized folder with all the files renamed to a specific format. The format is easy to customize by simply dragging the naming categories from one input box to the other.

File Organizer

As you can see in the image above, I chose to rename my files and keep them in one folder with the file name following the format Author – Year – Title. I did not add the journal to the file name, but could have easily done so by just dragging it down into the file name.

There’s an option to organize the files into sub-folders, however I chose not to do so. That’s just my personal choice even though I know colleagues of mine prefer to separate things into sub-folders by year.

Once I’ve picked how I want my files to be sorted and renamed, I go ahead and click apply. Folders get created, files get renamed and I’m done:

Renamed Filenames

These file names are much easier to understand and are categorised how I want them. This feature has not only organized my files into a folder with proper file names, but it will keep any new documents I add in the same orderly fashion. Neat huh?

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17 Responses to “An organized folder is a sign of a… file organizer”

  1. T. S. Says:


    it would be even neater if there was not only an option to copy all the files to a designated folder but to rename them in-place. I’ve got already a farily thought-through folder system which I would very much like to keep, but would nevertheless appreciate Mendeley to rename some files within these folders in a more meaningful way.

    That feature would make Mendeley the most useful program to me ever!
    Cheers, T.

  2. Daniel Münch Says:

    The file organizer is indeed a very nice feature if it would just be a bit more flexible… 😉

  3. Carl Anderson Says:

    This is probably as good an opportunity as any to note that although the screenshots above show you are organizing files on OS X, there is still (I think) an outstanding bug that prevents folder watching and file reorganizing from working on external volumes under OS X (though the features do work on a local volume, as shown in the above examples). I find this particularly unfortunate, as it is precisely because my OS X machine at home has a very large number of PDFs (such that they are happier living on an external volume) that would definitely benefit from folder watching/file reorganizing — but (at this time) can’t.

    However, the features seem to work happily on the Windows machine in my university office. I would only add that, for file reorganization, being able to define custom subfolder types (perhaps based on tags or collections or something?) would be very handy indeed; more so, I think, than creating subfolders based on author, journal (though what happens to files that aren’t journal articles in this case?), or year (and does anyone really want subfolder hierarchies based on title?). I realize that subfolder hierarchies based on tags or collections would quickly run into trouble in cases where documents had multiple tags or belonged to multiple collections, but perhaps Mendeley desktop could actually simply store the file in one place and automatically generate aliases/shortcuts to that “master file” that could be stashed elsewhere in the folder hierarchy? Such feature tweaks might really make these capacities start to fly … :)

  4. Joao Says:

    An essential missing feature is when you delete an entry inside Mendeley the corresponding file should also be deleted from the organized folder.
    Until this happens, the folder can quickly become disorganized unless you manually delete all these files.

    Nevertheless, this folder organization feature is what converted me from EndNote.

  5. Xenko Says:

    Now if only Mendeley could search for duplicates… and move entire libraries from one computer to another it would be perfect.

  6. MS Says:

    Yes it’s a very nice feature, but it lacks something very simple: The organized files in the specified directory should be changed/deleted whenever its library entry changed/deleted. There is no way you can track manually those files and it should be no problem to delete since they are originally copies from another directory outside Mendeley’s control. So unless you leave that folder grow infinitely and have duplicates or old no longer needed files, you have to manually check each file to see if it still exists in the library!

  7. lorenz Says:

    Really liked the new mendeley desktop software, recognized 100% of my newly added papers with correct meta tags like doi, authors, journals etc., big improvement to the previous version!

  8. Fletch Says:

    This feature is a great addition to Mendeley, and I’ve been using it since I started using the program. However there does seem to be a problem with the way it handles renaming of papers within Mendeley and the subsequent organization of the files in the Mendeley papers folder. If you rename a paper within the program it seems that Mendeley will save a new copy of the file alongside the original. It even seems to do this in the course of typing the new title. The result is a folder full of several copies of the same file; each with an ever-more truncated version of the file name. i.e. Author-Year-Title.pdf , Author-Year-Titl.pdf , Author-Year-Ti.pdf

    I’m not sure if I can post a link in these comments, but here’s a screenshot of part of my Papers folder
    You can see what I mean from that snapshot

    I’ve posted about this in the feedback forums (currently ranked 18th) but it doesn’t seem to be getting picked up

  9. Sam Says:

    This is great and can save lots of time but I have two concerns.
    1. does this mean that you have duplicates of every file? Or can you simply delete all of the original files?
    2. I work on many different projects and prefer to make sub-folders linked to a topic or project, so that they are easily retrievable when I want to attach them in an email etc. Does Mendeley ‘File Organizer’ allow this?

  10. Oori Says:

    Hi Ricardo,
    I’ve started using Mendeley at home. We have a server where we drop our files (they are indexed by a full text browser). We use macfusion to map the directory to our mac (it’s an ftp server on a hosting company). I asked mendeley to monitor it, but when I drop files there, they are not added to the library.. any idea why a macfuse mounted library wouldn’t be monitored?


  11. rishabh Says:

    Hi All,

    I am in a fix after using this feature of renaming the files.
    I accidentally renamed all my files (probably very dumb). Now I want to restore their names. Is it possible ?
    Another side effect of the above action is that none of the hyperlinks to the files are working anymore.

    please advice


  12. nomatter Says:


    I am a bit confused by the organizer’s folder and downloaded folder. I am working with different computer, synchronizing files via Mendeley. However, The files are stored in separated folders. I cannot manage to change the ‘downloaded’ folder from the system. It is always loaded in ‘.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded’ (Ubuntu) or ‘/application/…/Mendeley Desktop/Downloaded’. In addition, the file names can not be changed.

    On the other hand, if you add PDF files locally, they will be stored in the specified folder in ‘File Organizer’. However, if you sync in another computer, they will go to ‘Downloaded’ folder.

    Any solutions to this?

  13. Benjamin Says:

    This is a great feature, but it would be even better if articles could be sorted by last author instead of the first few. It’s rare for me to have multiple papers that get sorted together with the way Mendeley currently organizes with “Author”, but I’d love to be able to have all the work coming out of a single lab put together.

  14. William Says:

    Yes, sort by last author does make sense for some disciplines, particularly scientific research. Until we get this implemented, you may want to try tagging all the papers from a given lab. This wouldn’t work automatically for all papers, but it would include papers from the lab where the PI may not have been the last author (for example, collaborations with other labs).

  15. Roberto Says:

    How about an option that takes away commas and dots from the file name? Is there really the need to keep all the coauthor names in the name of the file? I think only the first coauthor is enough to distinguish between files.

  16. Chris Smith Says:

    What we really need is volume and page numbers available as options to be added to the file name e.g. author_year_journal_vol_page. That’s probably the optimum for a coherent archiving system with a short file character name.

  17. Shreya Says:

    This is a good feature. However, a great addition will be if we can organize the files into subfolders based on the folders in Mendeley – I usually sort them according to context after importing, and it would be good if that structure could be maintained with the file system as well.