Zotero 2.0 added many new features including syncing and back-up using Zotero's servers, social-networking with People and Groups features, and other functions. It was released under the free software GPLv3 license. More information about the changes can be found at these web pages:

If upgrading from Zotero 1.0, it would be useful to read the information on upgrading here:

This Wiki page needs some updating following the release of Ubuntu, the 12.04 Oneric Ocelot long term support version, in April, 2012.

About Zotero

"Zotero [zoh-TAIR-oh] is a free, easy-to-use Firefox, Chrome & Safari extensions & standalone application to help you collect, manage, and cite your research sources."

Zotero is useful for students, researchers, teachers, and anyone who uses scholarly references in their writing. It can also be used to archive snapshots of web pages.

Zotero comes as a Firefox extentsion, Chrome and Safari connectors, and as Zotero standalone. The connectors give similar functionality from the other browsers as in Firefox.

An extension for the Firefox web browser (also for Flock and Netscape), Zotero makes it very easy to gather references from the internet. When you click on a Zotero icon in the Firefox address bar (the blue book icon in the screenshot below - you will see a different icon for different types of media), Zotero "grabs" the reference and stores it on your computer, automatically filling in the database fields. Zotero_screenshot_smaller.png

A Zotero icon appears whenever you visit a compatible website. Once captured, the reference data can be used whether your computer is connected to the internet or not.

Zotero provides different ways to organize and search though these references with Collections and Tags. There is a very robust Advanced Search that allows you to gather references in Saved Search folders. Files such as PDFs, word processing texts, spreadsheets, images, videos, etc. - any kind of file - can be associated with Zotero references, and Zotero makes it easy to save snapshots of web pages. Along with Zotero's playlist-like interface, these features let you use Zotero as a full-fledged "media library" for all of your research documents. You can take notes in Zotero, too.

Zotero data can be used in many different ways. Citations can be generated in a variety of bibliographic styles, such as APA, Chicago Manual of Style, IEEE, and MLA (full list here). Zotero can create bibliographies in HTML and RTF formats as well as generate reports, and there is a plugin allowing for integration with blogging software such as WordPress. In addition, there is a Zotero extension for OpenOffice.org, for managing citations and bibliographies directly in your Writer documents.

The Zotero project assures that its users will remain "...free to import and export content into and out of Zotero without worrying about being locked into a proprietary system." Produced by the Center for History and New Media at George Mason University, it has received funding from the United States Institute of Museum and Library Services, the Andrew W. Mellon Foundation, and the Alfred P. Sloan Foundation (see the About Zotero page). Zotero is licensed under the GPL, version 3.

To learn more about Zotero and see its features in action, you can watch the Zotero tour (flash video).

Installation (All versions of Ubuntu)

1. Check which version of Firefox you’re using.

  • Zotero works with Firefox 3 (full compatibility from version 1.06).

You can check which version of Firefox you are using and update it if necessary with Synaptic.

2. Install Zotero Firefox Extension.

3. Optional Install Zotero Standalone (currently requires Zotero Firefox? v3.0)

Currently there is a install script to set it up - Zotero Forums Standalone auto-installer page

Also Zotero Standalone can be installed from Zotero 3.0 download page where it can be decompressed and run manually from the folder. (don't for get to make file executable)

Using Zotero

Integration with OpenOffice.org

The Zotero extension for OpenOffice.org allows you to insert formatted citations and bibliographies right into Writer documents while you compose them. If you use a reference format that includes a bibliography, Zotero will update the bibliography as citations are added and removed.


To see how the extension works, you can watch this screencast (flash video), from the Zotero documentation. The screencast shows the extension being used with Microsoft Word, but the information applies to OpenOffice.org Writer, as well.

Installing the OOo extension

1. Install the OpenOffice.org extension from the Zotero website.

If you are upgrading to a newer version of the extension, make sure to uninstall the extension using the extension manager and to restart OOo before trying to install the new version.

Info <!> Note: In order to use the OpenOffice.org extension, Firefox needs to be open.

If you have any problems with installing or using the extension, check the troubleshooting guide.

Window management for the OOo extension

By default, the Zotero extension windows, such as the "Add/Edit Citation" window in the screenshot above, appear underneath the OOo Writer window. To fix this problem, so that the extension windows appear and remain on top, you can add some window management rules for the extension. The procedure for doing this differs depending on which window manager you are using.

Compiz (or "Visual Effects")

Visual Effects are enabled by default on systems that support this feature. To add window rules when using Compiz under GNOME,

  • First, install the compizconfig-settings-manager package, if you haven't done so already.

  • Open System -> Preferences -> Advanced Desktop Effects Settings and choose the Window Rules plugin.

  • In the Above field, add the following:

    • title=^Document Preferences$ | title=^Add/Edit Citation$ 
  • Then go to General Options, the Focus & Raise Behavior tab, and set Focus Prevention Level to Off.

To add window rules when using Compiz under KDE,

  • Open K Menu -> System Settings -> Window Behavior -> Window Specific

  • Click New...

  • In description type Display Zotero "Add/Edit Citation" window above OO Writer

  • From OO Writer, open a Add/Edit Citation window. Back in the Edit Window-Specific Settings dialog, click on Detect window properties and then select the "Add/Edit Citation" window. Make sure Match also window title is checked then click OK.

  • In the Workarounds tab, check Focus stealing prevention and select Force and None.

  • Click OK then Apply to save.

(For more information about window rules in Compiz, see: http://wiki.compiz-fusion.org/WindowMatching)


Metacity is GNOME's window manager. It is what is used when Compiz/Visual Effects are not enabled in Ubuntu. Metacity users can install devilspie and then add rules for the extension windows. For more information on using devilspie, see http://foosel.org/linux/devilspie

Additional Tips

Zotero is a powerful tool with many features that can be used in many ways. To discover how Zotero can work with your own research, make sure to look at Zotero's documentation, starting with the screencast tutorials.

Here are some additional notes that may be helpful for Ubuntu users, as well as users of other Linux distributions and other Unix-y operating systems:

Full-text indexing of attached files

Zotero stores attached files in individual, numbered folders in your Firefox profile, which is a hidden folder in your home directory.

It is possible to view files from within Zotero, by selecting the file in the center pane and clicking the Show File button at the top of the right pane. This will open the folder in which the file is stored in Nautilus.

However, it can also be useful to access files with Search, using a full-text indexing service. There are several options for this.

Zotero native
Zotero can index the contents of file attachments, so that the full text will be searched when terms are typed in the Zotero search box.
  • Activate this feature by clicking on the Actions menu in the Zotero window (the "gear" icon, cog.png). Choose Preferences... -> Search and then click on the Check for installer button.

  • Full-text search can make Zotero searches less responsive, so it might be necessary to adjust the settings.

The Tracker indexing and search tool can also be used to access Zotero files. Tracker will not index files in hidden directories. To work around this, you can move your Zotero data folder from its default location in your Firefox profile to a new folder that is not hidden, for example in your home folder, which Tracker indexes by default.

  • To move the Zotero data folder, begin by closing Firefox.
  • Then use Nautilus (Places -> Home Folder) to create a new, non-hidden folder (File -> Create Folder).

  • Now copy all of the files in the Zotero folder, located at /home/<user name>/.mozilla/firefox/<randomstring>/zotero/, into the new folder. Do do this, you will need to show hidden files in Nautilus, which you can do by clicking CTRL+H or by selecting View -> Show Hidden Files.

  • Lastly, tell Zotero where the new folder is located. Restart Firefox, open the Actions menu in the Zotero window (the "gear" icon, cog.png). Choose Preferences -> Advanced, and under Storage Location, select the Custom option. Then click the Choose... button and navigate to the new folder.

Once you've verified that Zotero knows where to find the files in their new location, you can delete the Zotero storage directory in your Firefox profile (this is useful if you've already added a large number of files and do not want to store two copies of everything).

Another option is the Beagle desktop search application. Beagle will index hidden directories if it is configured to do so. Thus, it's not necessary to move your Zotero data directory when using Beagle.

  • To configure Beagle, you can use the beagle-settings application.

  • Select the Indexing tab, and under General, click the Add button.

  • Then navigate to your Zotero storage directory in your Firefox profile folder (/home/<user name>/.mozilla/firefox/<randomstring>/zotero/storage). Only the storage sub-folder needs to be added.

Zotero native indexing can be used at the same time as Tracker and Beagle, so it's not necessary to choose.

Info <!> Note: full-text indexing will not work with all PDF files. Some PDFs contain plain text and others contain images. Image-based PDFs may or may not include a text layer (generally created using OCR). It is the text layer that is indexed, so for image-only PDFs, just the file name will be indexed. (Some image-only PDFs do include additional metadata, such as Author or Keywords, that will be added to an index. You can view a document's metadata in Nautilus, by right-clicking on the file, choosing Properties, and then selecting the Document tab.)

Note-taking with Zotero

  • An overview of Zotero's note-taking features

  • The notes screencast (flash video) is a good introduction to how to work with notes in Zotero.

  • Notes can be assigned tags and related to other items in your Zotero library. They can be added as attachments to existing Zotero items or as stand-alone, top-level items.
  • Starting with Zotero 1.06, it is possible to drag notes from the central Zotero pane and drop them directly into documents, including OOo Writer documents. Drag and drop of notes also works with Freemind, a mind-mapping application that is useful for creating outlines.

  • With Reports, it is possible to organize notes into an outline within Zotero, as well. Instructions here.

In the future, it should become possible to rearrange Zotero's layout so that, for example, notes can be taken in a sidebar while reading a document in the main Firefox window. At present, there is an option to detach the note from the Zotero interface with the Edit in a separate window button.


Zotero's note-taking features can be enhanced by adding plugins to Firefox that enable you to read different types of files right in your browser. See Firefox plugins for more information. A few supplementary notes:

  • To view PDF (and PS) files in Firefox with the GNOME Document Viewer, Evince, you can install the mozplugger (universe) application (see Evince Mozilla). Mozplugger works with many types of files in addition to PDFs. If you would prefer to use other Firefox plugins for other files (such as multimedia files) and limit mozplugger to PDF and PS files only, you can add a custom mozplugger configuration file to your Firefox profile.

    • Open your Home folder and enable "Show Hidden Files" in the View menu or by pressing CTRL+H.

    • Navigate to the .mozilla folder.
    • In that folder, create a new text file named "mozpluggerrc" (no quotes).
    • Paste the following text into the file and save:
      • # Configure file for MozPlugger 1.10
        # Based on version: January 4, 2008
        # This is a custom configuration file for MozPlugger, for opening
        # PDF and PS files with Evince. Copy the contents to ~/.mozilla/mozpluggerrc
        # For more information, please refer to the original configuration file,
        # at /etc/mozpluggerrc.
        ### Documents       ###
        application/pdf: pdf: PDF file
        application/x-pdf: pdf: PDF file
        text/pdf: pdf: PDF file
        text/x-pdf: pdf: PDF file
                repeat noisy swallow(evince) fill: evince "$file"
        application/x-postscript: ps: PostScript file
        application/postscript: ps: PostScript file
                repeat noisy swallow(evince) fill: evince "$file" 
    • Now completely close all instances of Firefox that may be running.

    • Look in the .mozilla folder for all occurrences of a file named pluginreg.dat. There will be up to three versions of the file: one copy in .mozilla, and another in either .mozilla/firefox (Firefox 2) or in .mozilla/firefox/<randomstring> (Firefox 3), or both places. Delete all versions of pluginreg.dat. It's OK to do this, the needed files will be regenerated when you start Firefox again.

    • To test that all is well, start Firefox and in the location bar, type about:plugins. You will see a list of all the plugins you've installed, including mozplugger for PDF and PS files. You should now be able to open and view PDFs in Firefox.

    • At present, you can open only one file at a time with this plugin, subsequent files will open but in separate windows. See: https://bugs.launchpad.net/ubuntu/+source/mozplugger/+bug/46017

  • For office documents, you can use mozplugger (see /etc/mozplugger for examples of what to add to your custom configuration file), but there is also another, specific plugin that works well, in the mozilla-openoffice.org package (universe).

    • By default, this plugin works with all OpenOffice.org file types (ODT, ODS, etc.).

    • You can also configure the plugin to open MS Word office files such as DOC and XLS. For instructions, see this Ubuntu Forums thread.

      • Note that this method involves editing the pluginreg.dat file. If you want to use mozplugger with evince, you should set that up first since it involves deleting pluginreg.dat.

Info <!> Note: Along with notes as described above, Zotero includes additional features specifically for taking notes on saved snapshots of web pages: sticky note annotations and highlighting.

  • Sticky notes are indexed by Zotero's native full-text search. However, they cannot be dropped into other documents or included in a report.
  • Sticky note annotations and highlights cannot be used with PDF files or any other file that is not a Zotero web page snapshot.
  • The annotations toolbar appears at the top of the Firefox screen even when incompatible files are viewed using a browser plugin. This is a known problem that ought to be fixed in the future. In the meantime, it is possible to hide the annotation toolbar completely, so that it does not appear when any documents are viewed (including web page snapshots). To do this, you can edit the userChrome.css file in your Firefox profile, adding the following lines:

    • /* Hide Zotero annotation toolbar */
      #zotero-annotate-tb {display: none;} 

    Again, this will hide the annotation toolbar for all documents, so you should not do this if you'd like to highlight and annotate your web page snapshots.

What people are saying about Zotero


A review by Ubuntu and Ubuntu Forums Staff Member bapoumba: http://bapoumba.wordpress.com/2008/03/13/zotero-a-browser-based-reference-manager/

Zotero on Linux.com (older review): http://www.linux.com/feature/57841

Discussions on the Ubuntu Forums



More threads can be found by searching.

Alternatives to Zotero

OpenOffice.org integrated bibliography database

OOo does include a bibliography database.


Bibus is a stand-alone database with OOo integration for managing references in Writer documents.

  • It has more support for customizing citation formats than Zotero at present.
  • It is integrated with PubMed for online research, but references from sources other than PubMed must be entered by hand.

  • It has been around longer so it seems that more OOo users have experience with it.

JabRef is a BibTeX-based bibliography manager.


CategoryOffice CategoryThirdPartySoftware

Zotero (last edited 2012-06-04 00:52:30 by balingupjer)