Research Papers Management With Zotero and Yandex.Disk

Zotero is an open-source Firefox plugin for managing research paper collections. You can use the online zotero storage (pretty small) or use a third-party sync application. I use Yandex.Disk for this purpose: 10 GB is quite enough for a moderate research library. Zotero can automatically fetch article metadata (author, year, etc.) from the web (as Mendeley and similar software do).

§ Prerequisites

You will need:

• Firefox (the latest version for Ubuntu 12.04 can be installed via the official PPA)
• Zotero plugin for Firefox
• Zotfile add-on for Zotero
• Yandex disk or Dropbox for syncing settings and the library between devices
• Optionally on an Android device: ** FolderSync Lite for syncing the library folder automatically ** RepliGo PDF Reader or another PDF reader. RepliGo PDF Reader is paid, but it can add annotations and is pretty smooth.

Zotfile is a feature-rich add-on for Zotero, but I use it for two purposes only:

• Rename and Move Attachments based on Zotero Metadata
• Extract Annotations from pdf files

After installation of Zotero and Zotfile you will need to restart Firefox.

I’ve created a Zotero folder in my Yandex.Disk with two subfolders: Data for the Zotero database and misc files, and Library for renamed PDFs. No additional internal structure in Library is used: I wanted a plain list of articles and books with the name template Author2010.pdf.

§ Configuring Zotero

Here I’d like to list several important options to change. You can toggle the zotero pane visibility with a shortcut (Ctrl+Shift+Z by default).

• Settings> Preferences> Advanced> General: Switch Status bar icon to None (now you can hide the plugin panel at the bottom of the Firefox window).
• Settings> Preferences> Search: Install plugins for PDF indexing (you also need them to extract metadata from PDF).
• Settings> Preferences> Advanced> Files and Folders: Set Base directory to ~/Yandex.Disk/Zotero, and the Zotero database Data Directory Location to ~/Yandex.Disk/Zotero/Data.

Now you will be asked to quit Firefox. Do it and move the old Data directory to a new location: move all data from ~/.mozilla/firefox/<random_string>/zotero/ to ~/Yandex.Disk/Zotero/Data.

Now start zotero again.

§ Configuring Zotfile

Zotfile has many options for renaming files based on article attributes: year, author, etc. I use the Author2010.pdf format, i.e., the first author’s family name and the full year.

• Settings> Zotfile Preferences set Location Of Files to ~/Yandex.Disk/Zotero/Library. Renamed article files will be moved there.

Set up the Author2010 format for renaming. In Settings> Zotfile Preferences> Renaming Rules set Format for all Item Types except Patents to {\%a}{\%y}. I’ve also set Maximum number of authors to 1 and removed the check at Add suffix when authors are omitted.

Some books are in djvu format, allow djvu handling: at Settings> Zotfile Preferences> Advanced Settings> Other Advanced Settings add djvu to Only work with the following filetypes.

§ Workflow

Now, instead of downloading a PDF file, I can save it to Zotero and retrieve metadata from the PDF automatically. Then I open the Zotero pane (Ctrl+Shift+Z by default), right-click the newly added item in the library, and choose Manage Attachments> Rename Attachments. This will rename the file according to the format defined in the zotfile preferences and move it to the Library subfolder. Double-clicking the item will open the file in Firefox’s embedded PDF viewer.

In almost all cases metadata is extracted and downloaded correctly.

§ Android side

Syncing with a mobile device is strongly needed. Otherwise, I need two-way sync for downloading annotated PDFs from the tablet back to the desktop computer. For this purpose I use the free app FolderSync Lite. This app can download and upload the whole folder to/from many cloud-based storage providers, Yandex.Disk among them. So, I set up a two-way sync of the Library subfolder.

For reading and annotating I recommend RepliGo PDF Reader. It is a paid application.

Screenshot: