Friday, March 1, 2013

going "all-in" with Zotero, Zotfile, & Zotpad (step-by-step)

Inspired by some recent posts and frankly, more than a little frustrated with some of the limitations I found in Mendeley, I finally went "all-in" for Zotero. Of course making this decision is only ever the first step. Next, I needed to set-up all my tools properly to ensure that the set-up worked for the workflow I intended. I started looking around and really couldn't find any step-by-step tutorials for setting up all three tools (at least not all in one place). Instead, details for setting up all three were often spread across many websites. So hope this step-by-step helps.

Before launching into the tutorial, let me explain why I'm abandoning my current Mendeley setup and moving to Zotero. More accurately, I should perhaps say moving back to Zotero. I had tried it long ago, but got seduced by some of Mendeley's features. For example, I think Mendeley is way ahead in the looks department and it still has the best in-app PDF reader (at least on the desktop); truth be told, this in-app PDF reader was one of the main reasons that I switched to Mendeley. Pretty, isn't it?

But since it came out, much better annotation tools have come out- especially for tablets so Mendeley's cool in-app PDF reader is much less important to me. Instead, I need to be able to read, annotate, and sync changes from my iPad back to my reference management software (whatever that may be)- something the Mendeley app doesn't do well and Zotero's Zotpad does much better.

Plus, I found Mendeley's reports features to be seriously lacking. Mendeley only generates "annotation reports" one article at a time; these "reports" are basically little more than individual extractions of annotations to a PDF. This way of reporting is not all that useful for academics who would probably rather see reports across several PDFs and in a better format for editing than PDFs.

For all these reasons, I think Zotero is a much more flexible and robust program. In summary, here are the main reasons I wanted to go back to Zotero:
  • I read on iPad so it's frustrating that the Mendeley app is just so bad. Since I have my own favorite annotating app (iAnnotate), I don't even need the Mendeley app to have annotation abilities, I just need to be able to easily open and update the attached file.
    • Right now, this process is incredibly clumsy in Mendeley; it works like this 
    • 1) Browse Mendeley's iPad app, 2) choose the article I want to read, 3) open iAnnotate and download the article, and 4) use iAnnotate's sync features to sync the file back to Mendeley. See here and here.
    • Moreover, the app takes forever to repopulate all the files.
    • Zotpad is much better than Mendeley's iPad app- Mendeley Lite
  • I love the reporting features in Zotero:

  • Zotero can create reports across several references:

here's an example:

  • I love the extract annotations feature in Zotero (using Zotfile) which extracts all annotations to a child note:

    So here's the step-by-step setup...

    Set up Zotero:
    • Under Preferences, choose to sync only the ref info (no files) in Zotero online. I do this because I store my PDFs in Dropbox so I don't have to pay for extra storage in Zotero's online account.
    • Zotfile allows you to move and rename PDFs to names that make sense rather than Zotero's hinky little naming convention. 
    • Zotfile also extracts annotations (a favorite and important feature)
    • Once you install Zotfile, you'll see additional preference options
    Step 3: Set up a folder in Dropbox where you will store your PDFs. To do this, open "Zotfile Preferences..."

    • I named my folder "Articles-Zotero"
    Step 4: Then set up a "Source Folder," a default folder where new articles to be imported into Zotero will go (it's kind of "watch folder," but not really since Zotero doesn't automatically import files from this folder)
    • according the Zotfile documentation, the Source Folder is the folder where "...Zotfile looks for the most recently modified (e.g. just downloaded) file..." for attaching new files.
      • The zotfile documentation further adds that "For Zotero Firefox, this option is set to the Firefox download folder by default. For Zotero Standalone, this option has to be changed on the 'General Settings' tab in the preference window (Zotero Actions -> ZotFile Preferences). The source folder can be set to any location but I generally recommend setting it to your browser's download folder such as ~/Downloads on the mac for most browsers."
    • I created a folder named "Articles-New" in Dropbox and basically, it seems to act at a kind of first place for Zotfile to look when you choose the "Attach New File" option. Otherwise, it doesn't seem to be that important.
    Step 5: Finally, decide how you want to rename your PDFs
    • I have Zotfile rename my articles as "Author-year-title"; remember this info.- it's important when you set up Zotpad later (see below).
    Get references out of Mendeley:
    1. Open Mendeley
    2. Since I have about 1000+ references in Mendeley, I found it better to export by collections (you could try to export all, but when I tried importing this full file, Zotero crashed); choose RIS as the export file format.
    3. Go back to Zotero and import each collection back in one at a time
      • each import may take a very long time if you have lots of stuff in Mendeley; what Zotero and Zotfile are doing is importing, moving, and renaming each file! More than once, I got a message that Zotero had stopped responding, just be patient, when the import is done, you'll get several pop up messages from Zotfile that a file has been successfully imported and renamed.
    Working on iPad:

    Step 1: Buy Zotpad ($9.99)
    Step 2: Open up the Settings, locate Zotpad and choose "Dropbox" as the file storage

    Step 3: In Advanced Dropbox Settings, select "Allow full access" and change the name of the file directory (in my case "Articles-Zotero"), see here. (Also make sure that the naming conventions in Zotpad match your naming conventions in Zotero!)

    Step 4: Finish setting up the Dropbox link by opening Zotpad. Zotpad will then try to open Dropbox to ask for permission to access Dropbox (the usual Dropbox app link request).
    • Then to read and annotate readings on iPad, do the following:
      • Open Zotpad
      • Browse to the file you want to read, click on the PDF (this opens the PDF, but without annotation options)
      • Choose "open in" and send to your PDF editor/annotator of choice
      • When you're done, repeat the process: "Open In…" and send back to ZotPad, which will recognize the file and update it on the Dropbox server. It's a robust system that really meets my needs, and doesn't tie you in to any particular annotation software."
    Here are some useful links and are in fact the ones that inspired this post: 


    1. thanks, this is great. is there a reason you use zotero standalone and not a browser plugin?

      1. Thanks for reading! I use the standalone version mostly because I use Chrome. A long time ago, I also remember that Zotero seemed to slow down Firefox quite a bit and was a memory hog (I think that was one of the original reasons I left Zotero). However, the standalone version syncs with the Firefox version easily. So if I'm using Firefox, I can just as easily use the Firefox version. Meanwhile, in Chrome, I have the Zotero bookmarklet installed ( and am trying out the Chrome connector (available from the Chrome web store for free). I'll be posting some updates so stop by again and of course, feel free to share your workflow!