Using the free reference management tool Zotero Managing References Using the free reference management tool Zotero Managing References

Overview Why use a reference management tool? Zotero functionality Creating your Zotero library Adding references to your Zotero library Managing your documents and references Creating bibliographies Using Zotero with MS Word

Typical researcher writing a paper… Source: flickr/toennessen

Problem statement… Your topic: article Your paper citations book conference paper Your topic: Your paper reference list/bibliography citations Lots of typing Lost references Mistakes Managing References 4

Use a reference management tool! article book conference paper Your article citations reference list/bibliography Zotero Managing References 5

Reference management tools Tools that help scholars to create and manage their lists of references for research projects. Most tools are designed to organize citations into specific formats for the preparation of manuscripts and bibliographies. Many search tools provide ways to download references into reference management tools.

Software options Free Subscription

Zotero Zotero is a free reference management tool, that is available as an add-on for the Firefox web browser. Standalone version for Chrome, Safari and Firefox The Firefox web browser can be downloaded for free at: http://www.mozilla.com/en-US/firefox/ Note: you need version 17 or newer; current version is 20 (May 2013) To download and install Zotero go to: http://www.zotero.org

Zotero functionality Zotero recognizes bibliographic information on books, journal articles, and other resources from websites and databases and extracts metadata from these sources. Store related PDFs, files, images, and links in your library Create a bibliography in Word or OpenOffice. Publish shared libraries for your organization, class, or research group

Before you can install Zotero, you first need to install the Firefox web browser. Firefox can be downloaded from: http://www.mozilla.com/en-US/firefox/new

Next, go to the Zotero website at http://www. zotero Next, go to the Zotero website at http://www.zotero.org and click on the red Download button. Managing References

Note that there are Download options: Zotero/Firefox and Zotero Standalone version for Chrome, Safari and Firefox. For this module, download Zotero 4.0 for Firefox. When the download is complete, a box will appear. Click on Install now.

Exercise 1 Open the Firefox web browser (version 17 or higher) Go to the website: www.zotero.org Click on Then click on Install Now After installation, restart Firefox

While in PubMed, open Zotero by clicking on the Zotero logo in the bottom right of the browser.

This will open the Zotero window within the browser This will open the Zotero window within the browser. The window has three columns that represent different levels of specificity for your references: The left column shows your Zotero libraries and collections as well as 'tags' (keywords) The middle column displays items contained within the selected library The right column displays information about a selected item. Left column Middle column Right column

Many of Zotero's features can be customized via the Zotero preferences Many of Zotero's features can be customized via the Zotero preferences. To access the Zotero preference window, open Zotero, click the actions menu button (the 'gear' icon) at the top of the left column and select the “Preferences…” option

Within Zotero you can create collections to organize your references. To create a new collection, click on the New Collection icon in the left column. A box will appear prompting you to name your new collection. Choose a name and click OK. Your collection will appear in the left column.

Exercise 2 In the Firefox web browser, click on the Zotero logo in the bottom right corner to open Zotero. In the left column, click on New Collection icon ( ) and name this collection artimisinin or another topic of interest to you.

Adding citations to Zotero You can add citations to your library in several ways: Manually enter citation information Import citation information for a single item Import citation information for multiple items Automatically cite web pages Add an item by identifier (ISBN, DOI or PMID)

To create a citation manually in Zotero, click on the New Item icon in the middle column. A pull-down menu will appear. Select the type of item you want to cite, here we select Journal Article. In the right column, you will find fields that are specific to the type of item you selected. Fill in those fields for your item.

Exercise 3 In Zotero, click on the New item icon ( ) in the middle column. Select Book Enter the following title, author, publisher and publication date: An Introduction to Medicinal Chemistry G.L. Patrick Oxford University Press, 2013 (or a book title to add to your subject collection)

Zotero is compatible with many databases, including PubMed Zotero is compatible with many databases, including PubMed. Note: you can open HINARI/PubMed or regular PubMed If you are looking at PubMed search results, a Save to Zotero icon will appear in the address bar of your browser. If you click on this icon, the citation information will be immediately added to your Zotero library. A full overview of databases and publishers supported by Zotero is available at: http://www.zotero.org/translators

If you open an individual PubMed entry, you will see a Save to Zotero icon in the address bar of the browser. By clicking on the icon, the Saving to My Library... message will appear and save the record to the open collection.

If you are on a page with a list of PubMed results, you will see a Save to Folder icon in the address bar of the browser. If you click on the icon, a box will appear with a list of all records to import. Select the records you would like to import and click on OK.

Exercise 4 Go to PubMed and do a search for articles about: artemisinin combination or a search of your choice When you are on the results page, click on the Folder icon in the address bar: Select some articles to import into Zotero and click on OK

To import citations for webpages into your library, click on the Create New Item from Current Page icon in the middle column. Information about the current webpage will automatically be saved. You can edit the information by clicking on the fields in the right column.

Exercise 5 Go to the World Health Organization website - www.who.int - or a website of interest to you. In Zotero, click on the Create New (Webpage) Item from Current Page icon in the middle column : Look at your Collection to confirm that the website url has been added.

Another way to add a new item is by using the Add Item by Identifier option of Zotero. You find this icon in the middle column. You can enter an ISBN, DOI or PMID. Zotero will look up the information and import it into your library.

Attaching files to items In Zotero, any type of file can be attached to an item. Items such as the PDF of an article or images can be opened in the Firefox window, while other file-types open in external programs. You can add attachments to items by clicking on the button in the middle column that looks like a paperclip: All files stored in the Zotero library are kept in a folder within the Firefox profile directory (unless another location is specified in the Advanced preference tab).

Creating bibliographies from Zotero

Creating bibliographies from Zotero To create a bibliography from Zotero, highlight one or more references and then right-click to select Create Bibliography from Selected Item. Then select a Citation Style for your bibliography and choose one of the following four Formats to create your bibliography: Save as RTF will allow you to save the bibliography as a rich text file, which can be opened for example in Word. Save as HTML will allow you to save the bibliography as a HTML file for viewing in a web browser. 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.

To create a Zotero bibliography: Select the items you want to include in the middle column. Next, right-click the selected items. Choose the option Create Bibliography from Selected Items, a new dialog box will appear.

In the new dialog box: From the drop down menu, choose the Citation Style you would like to use Choose the Format (RTF or HTML) to save your document Click on OK

This is an example of a Zotero bibliography that was created using the Harvard citation style and RTF as format.

Exercise 6 In Zotero, Select (check boxes) the items you have imported from PubMed in the middle column. Next, right-click on your mouse or touch pad Choose the option Create Bibliography from Selected Items, a new dialog box will appear. Choose the Citation Style you would like to use Choose the Format RTF Click on OK Open the saved document with MS Word

Word Processor Integration Zotero's Word and OpenOffice plugins allow users to insert citations directly from their word processing software. You can find a link to install the plugin on the Zotero homepage (www.zotero.org). After installation of the plugin you should see this row of icons in your Microsoft Word toolbar: These six buttons allow you to manage references and bibliographies in your Microsoft Word documents.

Click on Add a plugin for Word or LibreOffice.

From this page, download and install the Word for Windows Plugin (Firefox extension). Note that this plugin option only can be used with Firefox.

Location on Word toolbar In Word, click on the Add-ins option on the toolbar. This will display the Zotero Plugin.

Citing in Word - example

Using The Zotero Word Plugin If this is the first citation you have added to the document the Document Preferences window will open. Chose the bibliographic format you would like to use from the list and click OK. Click on the “Zotero Insert Citation” icon

Adding a Citation in Word Once you have chosen a format, the Add citation window will pop up. Sort through your collection in this window, select the item you would like to cite and click on OK. You can add the specific page number in the text box at the bottom of the window.

Generating a bibliography To generate a bibliography from all the items you have referenced, click the Zotero Insert Bibliography button ( ) on the Zotero toolbar in Word. The Edit citation ( ) and Edit bibliopgraphy ( ) buttons allow you to edit citations and bibliographies you have already inserted into your documents. Click inside a citation or bibliography and click either button to edit. Never use your word processor to edit citations! Anything you type into (or delete from) a citation using Word will be automatically reverted the next time Zotero updates your document.

Generating a bibliography The fifth button on the toolbar, Zotero Refresh, ( ) updates your references to any changes in your Zotero collection. The sixth button on the toolbar ( ) will open the Document Preferences window again, allowing you to change your bibliographic style instantly.

Citation Styles A core feature of Zotero is its ability to automatically format citations and bibliographies. By default Zotero comes with a selection of popular styles (such as APA, Harvard and Vancouver), but many more are available through the online Zotero Style Repository at: http://www.zotero.org/styles Visit the Style Repository and click the “[Install]” link next to the style you wish to install.

Zotero Citation Style Repository Click on the “[Install]” link next to the style you wish to install.

Which citation style to use? Most journals provide information on which reference style to use in their “Instructions to authors”. Look for the heading “References”. The Mulford Library Instructions to Authors in the Health Sciences Guide provides links to web sites which provide instructions to authors for over 6,000 journals in health and life sciences: http://mulford.meduohio.edu/instr/

Zotero web account On www.zotero.org you can create a Zotero account. You need a Zotero account to synchronize your library, participate in groups, or post to the support forums. Data synchronization transfers library items, notes, links, tags, etc.—everything except attachment files—between your local computer and the Zotero servers, allowing you to work with your data from any computer with the Zotero extension. It also allows you to view your library online on www.zotero.org. To synchronize your data with the Zotero web server, open Zotero's Sync preferences tab and enter your login information in the Zotero Sync Server section.

Zotero Online Library

Zotero Groups Zotero Groups provide a way to share collections with a class, work with colleagues on a project or keep track of conversations in a specific field of research. Groups can be private or public. To create a group in Zotero: Click the New Group icon located in the top left corner of the left column in Zotero and follow the instructions.

Zotero Support On the Support page on the Zotero website (http://www.zotero.org/support/), which is available in several languages, you can find documentation on additional features of Zotero as well as Frequently Asked Questions and a number of screencast tutorials.

http://www.zotero.org/support/screencast_tutorials Zotero Screencasts demonstrate many of the basic functions of Zotero, such as adding references, managing your library, and how to use Zotero in Word.

References A Beginner’s Guide to Using Zotero - UBC Biomedical Branch Library. Available at: http://www.slideshare.net/giustinid/beginners-guide-to-zotero. Zotero Quick Start Guide. Available at: http://www.zotero.org/support/quick_start_guide.

This module initially was developed by: Ingeborg Nagel, MSc Information Specialist Royal Tropical Institute (KIT) The Netherlands Updated 2013 02