Zotero

Citation managers

jdorner@library.berkeley.edu (Jennifer Dorner) — Wed, 05 Dec 2012 16:14:01 -0800

Reference managers (also called citation managers or bibliographic management software) offer a way to save, organize and manage references. Many work with word processing software to format in-text citations and bibliographies for papers and theses, allow you to share references, and enable you to attach or link PDFs to a citation record.

Wikipedia comparison of reference management software

RefWorks

Free to UC Berkeley users
Web-based: use at any computer with internet access
Format bibliographies in Word
Import citations from RSS feeds
Use UC-eLinks to find the full text of articles from within RefWorks
Share lists of references or create a group account for co-editing

Zotero

Free (up to 300 MB web storage) browser extension
Sync Zotero to access your library from any computer with internet access
Format bibliographies in Word and OpenOffice
Capture citation data from PDFs and web pages
Share and collaboratively edit lists of references

Mendeley

Free (up to 1 GB web storage) software/web hybrid for PC, Mac, Linux
Format bibliographies in Word or Open Office
Sync PDFs to your web account for online access
Capture citation data from some PDFs
Search and annotate PDFs
Share and collaboratively edit lists of references

EndNote

Discounted to UC Berkeley users
Desktop-based software (plus EndNote Web)
Format bibliographies in Word or Open Office
Capture citation data from some PDFs
Annotate PDFs
Use UC-eLinks to find the full text of articles from within EndNote
Share lists of references with other EndNote users
See our EndNote Support page for tutorials and additional information

Getting Started with Zotero

jdorner@library.berkeley.edu (Jennifer Dorner) — Tue, 11 Dec 2012 09:44:09 -0800

Zotero was first developed as a Firefox extension and can be quickly added to Firefox by visiting zotero.org and clicking on the red "Download Now" button. Click the “Zotero 3.0 for Firefox” link. After installation, restart Firefox. You should now see the Zotero logo () in the status bar in the right bottom corner of your Firefox browser window and click to launch.

[Zotero "Standalone" works with the Firefox, Chrome, or Safari browsers via "connectors." More information can be found at http://www.zotero.org/download.]

Collections: The left column includes My Library, which contains all items. Clicking the button above the left column creates a new collection, a folder into which items rleating to a specific project or topic can be placed.

Below that is the tag selector, where tags assigned to items can be added or removed.

Items: The items pane displays a list of all the items in each collection with icons that indicate the type of item (book, article, thesis, screenshot, etc.).

Item Details: This pane displays the bibliographic information that was imported by Zotero for each item. There are also options to add additional notes, attachments, links to the original sources, tags, and subject headings.

Options for importing records

jdorner@library.berkeley.edu (Jennifer Dorner) — Tue, 11 Dec 2012 09:47:19 -0800

Importing from a Resource

After Zotero is installed, you will notice that when searching article databases, library catalogs, web search engines, and other resources, icons are added to the address bar of your browser.

The article, book, or page icons in the address bar indicate you are viewing a single item, and clicking on that icon will import the information into your Zotero collection.

Verify the information has correctly been imported before moving on.

If a folder appears in the address bar when you view a list of results, click on the folder to reveal a list of the items that appear on that page, then check the ones of interest and click on OK. This will import the results into your Zotero collection. Verify the information for each entry has correctly been imported before moving on.

Importing Manually

Importing citations into your Zotero collections does not always work without a hitch. If for some reason an icon doesn't appear in the address bar or if the information isn't importing properly, you may want to use another option.

	Use this option to manually add an item. Select the item type from the drop-down menu and enter the item's bibliographic information in the item details pane.
	Use this option to create an item from the current web page. If "Automatically take snapshots when creating items from web pages" is enabled in the General tab of your Zotero preferences, a copy (or snapshot) of the web page will be saved to your computer and added as a child item. To view the saved copy, double-click the snapshot.
	If you already know the ISBN, Digital Object Identifier (DOI), or PubMed ID of the item, enter it using this option.

Importing from other Tools

To import libraries from other reference management tools into Zotero, start by exporting the bibliographic data from your other software program. Then, in Zotero, click the gear icon () and select “Import…”. Browse to your file, select it, and click the “Open” button. This should import the exported items into your Zotero library.

Zotero can import the following bibliographic file formats:

Zotero RDF
MODS (Metadata Object Description Schema)
BibTeX
RIS
Refer/BibIX
Unqualified Dublin Core RDF

If you want to transfer entire Zotero libraries between different Zotero installations, you should use Zotero's sync functions, rather than the import/export function.

Organizing Your Library

jdorner@library.berkeley.edu (Jennifer Dorner) — Tue, 11 Dec 2012 10:59:48 -0800

In addition to storing bibliographic information, Zotero can save links to the full text, full text attachments, tags for organizing your content, snapshots of pages, notes about the items, and also stand-alone notes.

Tags

When you import items from databases, the subject descriptors attached to the items may be imported as tags. You can edit them, delete them, or add your own tags to each item. All tags are displayed in the bottom of the left column and the tags for each item are displayed in the item details column when the item is selected. Tags can be edited in both locations.

Notes

Child Notes - To create a note attached to an item, select the item from the list in the center column and either click the “New Note” button at the top of the center column () and select “Add Child Note”, or go to the “Notes” tab in the right-hand column and click the “Add” button.

A note will be created as an attachment to the item (it will also show up under the “Notes” tab), and a note editor will appear in the right-hand column. You can create a dedicated window for the editor by clicking the “Edit in a separate window” button at the bottom of the editor. Text in notes is saved as you type.

Zotero will sometimes automatically import information from a resource, such as a table of contents or abstract, into the notes of an item. Use the editor to change or delete these entries.

Standalone Notes - Standalone notes are not directly related to any item in your library, and will appear in the list of items in your library. To create a standalone note, click the “New Note” button and select “New Standalone Note”.

Copying and Pasting Content into Notes

With Zotero for Firefox, you can also create notes directly from the webpage you're visiting in Firefox. Highlight the text you want to copy into a note, right-click (ctrl-click on OS X), select “Zotero” in the pop-up menu, and select “Create Zotero Item and Note from Selection”. This will create a new “Web Page” item in your library for the visited webpage, with a note containing the selected text.

Attachments

You can set up your Zotero preferences so that when you import bibliographic information, depending on availability Zotero will also import a link to the item (), a snapshot of the item (), or the full text of the item. These appear as child items attached to the items listed in the middle column.

Searching Collections

Zotero searches citations, notes, and attached PDFs for your search term. Click on search () icon to pull up the Advanced Search Screen.

Your Zotero Files

jdorner@library.berkeley.edu (Jennifer Dorner) — Fri, 14 Dec 2012 12:08:40 -0800

If you are using the Firefox plugin version of Zotero, by default your Zotero library is stored in the 'zotero' directory of your Firefox profile. The easiest and most reliable way to find your Zotero data directory is by clicking the “Show Data Directory” button in the Advanced tab of your Zotero Preferences window.

Syncing Your Data and Files

All of the item information, notes, and attachments imported into your Zotero collection are stored locally in this directory on your computer. If you would like to be able to access your collections from any computer connected to the Internet, then you must register with Zotero for an account and sync your data between your computer and Zotero's servers. Zotero provides 300MB of free storage.

Data Syncing

Everything in your collections, including notes, links, and tags, will be saved to the server, except attachments.

After you have registered with Zotero, open Zotero's Sync preferences tab and enter your login information in the Zotero Sync Server section. Each time changes are made to your Zotero collections, Zotero will automatically sync your data. You can disable automatic syncing in the preferences window. You can sync manually at any time by clicking the “Sync with Zotero Server” button () on the right-hand side of the Zotero toolbar.

By default, Zotero will merge your local Zotero library with your library on zotero.org—any changes you make in one place will be applied to the other and on all other synced computers. If an item has changed in multiple places between syncs, you'll receive a conflict resolution dialog asking which version you'd like to keep. In the rare case that you want to completely overwrite your server library with the contents of your local library or vice versa, you can use the Sync Reset Options.

File Syncing with Zotero

Data syncing syncs library items, but doesn't sync attached files (PDFs, audio and video files, images, etc.). To sync these files, you can set up file syncing to accompany data syncing, using Zotero File Storage. Each Zotero user is given 300 MB of free Zotero File Storage for attached files, with larger storage plans available for purchase.

File Syncing with WebDAV

Another option for remote storage of files is to use a WebDAV service. Zotero does not provide support for third party WebDAV providers and when you set it up, you should make sure to use the "Verify Server" option to ensure that Zotero can successfully verify the WebDAV account.

One WebDAV service option is CloudMe, which provides 3GB of free storage. After you create your account at CloudMe, create a folder called zotero.

Then, in Zotero preferences, under "Sync", do the following:

1. select http:// (not https://)
2. type in webdav.cloudme.com:80/[user_name]/xios/Documents (your user name goes into the URL)
3. enter your CloudMe user name
4. enter your CloudMe password
5. click "verify server"

Creating a Bibliography

jdorner@library.berkeley.edu (Jennifer Dorner) — Mon, 10 Dec 2012 16:02:11 -0800

Setting your Citation Preferences

Before you create a bibliography, you should choose the citation style that you prefer to use. Click on the () icon and choose Preferences. Under Export, choose an output style from the list.

Creating a Simple Bibliography From your Item List

Quick Copy - Select titles in your item list and drag and drop them into an open word processing file.

Right-Click to Create Bibliography - Select one or more items from the list you want included in the bibliography and then right-click (or control-click on Macs) to select “Create Bibliography from Selected Item(s).”

Then select a citation style for your bibliography format and choose one of the following four ways to create your bibliography:

Save as RTF will allow you to save the bibliography as a rich text file.
Save as HTML will allow you to save the bibliography as a HTML file for viewing in a web browser. This format will also embed metadata allowing other Zotero users viewing the document to capture bibliographic information.
Save to Clipboard will allow you to save the bibliography to your clipboard to paste into any text field.
Print will send your bibliography straight to a printer.

Integrating Zotero into Word or OpenOffice

Installing the Zotero word processor plugin will allow you to insert citations as you are writing your paper using Microsoft Word or OpenOffice. After it is installed, a toolbar will be added to your word processing program. [In MS Word 2010, the toolbar appears in the Add-Ins tab.]

	Insert a new citation in your document at the cursor location.
	Edit an existing citation. You have to place the cursor inside the relevant citation before pressing this icon.
	Insert a bibliography at the cursor location.
	Edit an existing bibliography.
	Refresh all citations and the bibliography, updating any item metadata that has changed in your Zotero library.
	Open the Document Preferences window, e.g. to change the citation style.
	Remove Zotero field codes from the document. When Zotero inserts a citation or bibliography, it does so by using a field code. This field code allows Zotero to later recognize and automatically update the citation or bibliography (e.g., in numeric styles, citations have often to be renumbered when additional items are cited). Removing the Zotero field codes prevents any further automatic updates of the citations and bibliographies. Note that removing field codes is irreversible, and should usually only be done in a near-final copy of your document.

When creating your document, when you get to a point where you want to add a citation, click on the insert citation button in the toolbar and then search for the citation in your collection.

To generate a bibliography from all of the items you have referenced, click the Zotero Insert Bibliography button.

Getting Additional Help

jdorner@library.berkeley.edu (Jennifer Dorner) — Tue, 11 Dec 2012 11:30:28 -0800

More complete documentation, along with instructional videos, is available at Zotero's web site. The Library sometimes offers workshops on Zotero and other bibliographic management tools. We will do so "on demand" if a minimum of 5 students will be in attendance. You can also email questions to Jennifer Dorner at Doe Library or David Eifler at the Environmental Design Library.

"Zotero Standalone" also works with Firefox, Chrome, or Safari, but is not embedded in the browser. If you choose to download the standalone version, you'll also need to download the Zotero connector for the browser that you are using.

Adding UC-eLinks to Zotero

In the Preferences window, under the "Advanced" tab, add the URL for UC-eLinks as shown: http://ucelinks.cdlib.org:8888/sfx_local. Click on OK.

This will make searching for the full text easier.

When you want to retrieve an item not already stored in your collection, click on the green arrow above the Item Details window and select "Library Lookup" which will look up the citation via UC-eLinks.