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About Zotero

[http://www.zotero.org/ "Zotero] [zoh-TAIR-oh] is a free, easy-to-use Firefox extension to help you collect, manage, and cite your research sources."

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

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 the Zotero icon in the Firefox address bar (the small blue book icon in the screenshot below), Zotero "grabs" the reference and stores it on your computer, automatically filling in the database fields. A Zotero icon appears whenever you visit a [http://www.zotero.org/translators/ compatible website].

attachment:Zotero_screenshot.png

The reference data can then be used whether your computer is connected to the internet or not. Zotero provides different ways to organize and search though the references, and it is possible to associate files and notes with each entry. The data can be exported in a variety of formats, such as Chicago Manual of Style, APA, and MLA ([http://www.zotero.org/documentation/citation_formats full list here]) and to different kinds of documents. For example, there is a Zotero extension for OpenOffice.org for adding citations and bibliographies directly to documents (AKA "Cite While You Write").

The [http://www.zotero.org/videos/tour/zotero_tour.htm Zotero tour] (flash video) is a good introduction to Zotero’s features.

Installation (All versions of Ubuntu)

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

  • Zotero works with Firefox 2 (all versions) and Firefox 3 (full compatibility from [http://www.zotero.org/blog/zotero-106-now-available/ version 1.06]).

    • Warning /!\ Zotero does not work with the default version of Firefox in Ubuntu 8.04 Hardy Heron, i.e., 3.0~b5+nobinonly-0ubuntu3. Warning /!\ Please make sure to check which version of Firefox is installed on your computer.

  • You can check and update Firefox if necessary using [wiki:SynapticHowto Synaptic].

2. Install Zotero.

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, then Zotero will update the bibliography as citations are added and removed when you click on the extension's "Refresh" button.

attachment:OOo_screenshot.png

Installing the OOo extension

1. Download the OpenOffice.org extension from the [http://www.zotero.org/documentation/openoffice_integration Zotero website].

  • It will be a file named Zotero.oxt. Make sure to notice where the downloaded file is located (which folder).

2. Restart OpenOffice.org.

  • If you use the OpenOffice.org quickstarter, which puts an icon into the notification area of the GNOME panel, right-click on that icon and choose "Exit Quickstarter." Then start OOo again.

3. Install with the OOo Extension manager.

  • Open the Extension Manager (Tools -> Extension Manager) and select "My Extensions" then click the "Add" button. Navigate to the folder where Zotero.oxt is located, and choose Open.

4. Restart OpenOffice.org (again). You should see the Zotero toolbar. It can be moved to whichever part of the screen you prefer.

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

If you have any problems with using the extension, check the [http://www.zotero.org/documentation/openoffice_integration troubleshooting guide].

Additional Tips

Full-text indexing of attached files

Zotero stores attached files in individual, numbered folders that cannot be accessed readily with a file manager like Nautilus. However, the files can be located with a full-text indexing service. There are several options for this.

Zotero native
Zotero can index the contents of files 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, attachment: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.
    • Tracker

    The [wiki:MetaTracker Tracker] indexing and search tool can also be used to access Zotero files.

  • Tracker will not index [http://library.gnome.org/users/user-guide/2.20/nautilus-hidden-files.html.en files in hidden directories]. One workaround for this is to 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 idexes by default.

  • To move the folder, open the Actions menu in the Zotero window (the "gear" icon, attachment:cog.png). Choose Advanced, and under "Storage Location," select the custom option and select or create an alternative folder.
    • Beagle
    Another option is the [wiki:Beagle 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 then navigate to your Zotero storage directory in your [http://support.mozilla.com/en-US/kb/Profiles Firefox profile folder] (/home/<user name>/.mozilla/firefox/xxxxxxxx.default/zotero/storage).

    • 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 [wiki:OCR OCR]). It is the text layer that is indexed, so image-only PDFs will only have the file names and whatever metadata they may contain indexed. (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

    To make the most of Zotero notes, you can install Firefox plugins that enable you to read various kind of files from within your browser. There are many options. For example, it is possible to use an application called [https://launchpad.net/ubuntu/+source/mozplugger mozplugger] (universe) to read PDF and other files in Firefox (see [wiki:EvinceMozilla Evince Mozilla]). There is also a [https://launchpad.net/ubuntu/hardy/+package/mozilla-openoffice.org plugin for OpenOffice.org] (universe) for office documents, which can be [http://ubuntuforums.org/showthread.php?t=94384 configured manually] to open DOC, XLS, and PPT files.

    Info <!> Note: Zotero includes additional features for taking notes on saved snapshots of web pages: [http://www.zotero.org/documentation/archive_the_web?s=annotation 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 [https://www.zotero.org/trac/ticket/607 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 [http://support.mozilla.com/en-US/kb/Editing+configuration+files edit the userChrome.css file] in your [http://support.mozilla.com/en-US/kb/Profiles 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

    Reviews

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

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

    How one graduate student has been using Zotero: [http://gradhacker.blogspot.com/2008/03/zotero-review.html http://gradhacker.blogspot.com/2008/03/zotero-review.html]

    Discussions on the Ubuntu Forums

    [http://ubuntuforums.org/showthread.php?t=759938 http://ubuntuforums.org/showthread.php?t=759938]

    [http://ubuntuforums.org/showthread.php?t=698734 http://ubuntuforums.org/showthread.php?t=698734]

    More threads can be found by searching.

    Alternatives to Zotero

    OpenOffice.org integrated bibliography database

    OOo does include a [http://wiki.services.openoffice.org/wiki/Bibliographic bibliography database].

    [https://wiki.ubuntu.com/Bibus 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 [http://en.wikipedia.org/wiki/PubMed 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

    JabRef is a [http://en.wikipedia.org/wiki/BibTeX BibTeX]-based bibliography manager.

    CategoryDocumentation