On Keeping an Organized e-Library

A few months ago, I had around 600 journal articles and 100 books scattered throughout multiple folders in my computer. The pdfs were named with the last name of the most relevant author and some arbitrarily chosen keywords from the title. It goes without saying that looking for relevant information in this mess I called library was a painful process. Even deciding where to place a given pdf was difficult as the contents could be related to multiple, somewhat independent topics; for instance, a paper on classifying EEG signals for brain computer interfaces could easily be put under a machine learning, signal processing, or BCI folder. Once a paper was added to my library folder, I would rarely revisit it again; in fact, it was easier sometimes to just google some keywords to find the paper again.

One day, my coworker M introduced me to Mendeley, a program he used to maintain an organized paper library. I knew that software tools for this type of problem existed, but I never bothered to try some of them to find the best fit. In previous years, I had used Zotero to assemble a Bibtex bibliography file from some pdfs; I even tried to use it for general file organization during my last co-op, but I stopped out of laziness since adding papers from the browser was a little tedious. At first, I was skeptical, but after seeing M’s workflow and trying it on my own, I have to say that Mendeley changed the way I work for the better; good-bye poorly name papers inside messy folder structures!

I use Mendeley for mainly three tasks:

  1. Automatically rename papers at download time
  2. Organize papers by topic, field, project, etc
  3. Share reading lists among individuals or groups I work with

These features come in handy at work. At my lab, we have a reading requirement of 2-5 papers per week, which can be a little daunting at first; however, with Mendeley, adding and organizing papers in my library is fairly straightforward. By keeping all of my papers in a single Dropbox folder that is managed by Mendeley, I can even read my books/articles on my tablet! Android has an app called Referey that uses the database file from Mendeley to link the document entries to their respective pdfs stored in the tablet. Setting up both Mendeley and Referey is not complicated; the steps are outlined below.

Setting Mendeley to automatically rename files for you

Unfortunately, publishers name articles following an arbitrary and obscure notation; for instance, IEEE Xplore named a paper on single trial EEG classification as “06739167.pdf”. Even worse, none of the publishers agree on a common naming format. Mendeley solves this issue by automatically extracting relevant metadata from files and renaming according to standardized convention. To do this (assuming you don’t already have a Mendeley account):

  1. Create a Mendeley account at http://www.mendeley.com
  2. Download and install the desktop application
  3. Open your new Mendeley application and sign in using your credentials
  4. Go to Tools and then Options
  5. Go to the File Organizer tab and check the following options:
    • Organize my files. Browse to a folder where you want to keep your papers
    • Rename document files. Use the “author – paper – year” format
  6. Go to the Watched Folder tab
  7. Select the same folder from step 5.a
  8. Click on Apply and Ok

Now, whenever you download a new paper, put it in the watched folder. Mendeley will attempt to extract the metadata from the pdf and will rename it accordingly. If by any reason this fails, you can manually edit the metadata and Mendeley will rename the file for you once you are done. The metadata can be accessed on the right pane of Mendeley when you select the paper in the browser.

Organizing papers:

Mendeley has two main ways to keep your papers organized: tags and subfolders. I believe that tags are superior since papers can have multiple tags but can only belong to a single folder. For example, a SSVEP classification paper could be tagged as “BCI”, “SSVEP”, and “Machine Learning.” Here is how you do the tagging:

  1. Select the paper in the Mendeley browser
  2. In the right pane, click on the Tags textbox
  3. Type the tag name you want. If it already exist, an autocomplete box will appear
  4. Separate tags with a semicolon

To search for papers with multiple tags, use the Filter by My tags on the panel on your lower left and ctrl+click on the desired tags. Alternatively, you can use the search box by typing “tag: tagname” multiple times.

Sharing reading lists with your coworkers

You can share your new downloaded papers with your coworkers by sending the citation details as an email or as group contribution

  • Sending paper details as an email:
    1. Right click on the paper entry in the Mendeley paper browser
    2. Select send as email
    3. Fill in the details and send it
  • Contributing paper to a group assuming you have been invited to it already:
    1. Select the papers you want to share
    2. Drag and drop them on the group (located on the Groups section in the left top panel)
    3. Click on the Sync button
  • If you want to add papers from a group
    1. Go to the group page (click on group name located on the Groups section in the left top panel)
    2. Drag and drop the paper to your library
    3. Since the pdf is not shared, they may have to search for it themselves. You could always have a shared folder somewhere as well.
    4. Mendeley will automatically link the citation from step 1 to the new pdf added. If not click “tools > check for duplicates”
    5. You may have to manually edit the documents metadata if the extraction and linking fails

You can share your notes and highlights only if they were added in the group entry of the document; the annotations won’t sync if you added them to your personal document entry. This makes sense to me because I may jot down some notes that may unnecessarily clutter the paper for the rest of the group.

Setting up Referey:

Referey is an Android app that uses the Mendeley database file to pair the pdfs stored in the tablet with the respective document entries; this assumes that the pdfs are named the same both in your desktop and in your table (not a problem with Dropbox)

  1. Synchronize your libary folder with your tablet. I use Dropsync for this
  2. Find the Mendeley database file in: C:\Users\user\AppData\Local\Mendeley Ltd\Mendeley Desktop. It should be a file with this format: your_email@www.mendeley.com.sqlite
  3. Copy the file to your tablet. I do this with a Windows task scheduled nightly that copies this file to a Dropbox folder
  4. In the Referey app, set the database path to the full location of the file you just copied. It should be something like: /storage/sdcard0/…
  5. In addition, set the PDF folder path to the location of your pdfs. It should be something like: /storage/sdcard0/…

If everything is set up correctly, you should now be able to browse your pdf library from Referey.


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