Reference Management Software Tools
Zotero (Open Source)
Overview
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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
Appendix -Standalone Version 4.0 for
Windows
Problem statement…
Your topic:
article
article
article
article
Your paper
citations
book
book
conference
conference
conference
paper
paper
paper
• Lots of typing
• Lost references
• Mistakes
reference list/bibliography
Use a reference management tool!
article
article
article
article
Your article
citations
book
book
conference
conference
paper
conference
paper
paper
Zotero
reference list/bibliography
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 (open source) reference
management tool, that is available as an add-on
for the Firefox web browser.
• Standalone version for Chrome, Safari and
Firefox browsers
• 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 29 (May 2014)
• 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/
Next, go to the Zotero website at
http://www.zotero.org and click on the
red Download Now button.
Note: since both Firefox and Zotero
are open source programs and linked
to each others’ programming, it is best
to download Zotero from Firefox.
Note that there are Download options: Zotero/Firefox and
Zotero Standalone version for Firefox, Chrome and Safari.
For this module, download Zotero 4.0 for Firefox (cloud
based version). When the download is complete, a box will
appear. Click on Install now.
Later in the tutorial, we will download the Standalone
(Windows) version.
In Firefox, this Software
Installation query may
appear. If so, click on Install.
Click on the Restart Now
button to install Zotero.
Zotero has been loaded and is
accessible by clicking on the Z in
the Firebox toolbar.
Registering for Zotero is optional.
Exercise 1
• Open the Firefox web browser (version 17
or higher)
• If necessary, download Firefox:
www.mozilla.org/en-US/
• Go to the website: www.zotero.org
• Click on (preferably) Zotero for Firebox
• Then click on Install
• After installation, restart Firefox
Zotero – Initial View/Options
While in PubMed (or online), open
Zotero by clicking on the Z logo in
the right corner of the toolbar.
Note: in older versions of Firefox,
this will be in the bottom right of the
browser window.
Zotero
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
Click on the actions menu button
(the 'gear' icon) to view options
such as Import, Export, RTF Scan,
Support and Documentation…
Open the ”Preferences…” option.
Many of Zotero's features
can be customized via the
Zotero Preferences.
Within Zotero’s My Library, you can create collections to organize your references. 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 Z
logo in the right corner of the Firefox toolbar
to open Zotero.
• In the left column, click on New Collection
icon (
) and name this collection
artimisinin or diabetes AND developing
countries or another topic of interest to you.
Adding citations to Zotero
• You can add citations to your library
in several ways:
–
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–
–
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 drop-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 required 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. Note: you can open HINARI/PubMed or
regular PubMed
If you are looking at PubMed search results, a Send to
drop down menu with a Send to Zotero using “PubMed”
option will appear in the address bar of your browser. If
you click on this icon, the citation information will be
immediately added to your collection in Zotero. Note the
other Save to Zotero options.
Note: If you have not opened Zotero and opened the
collection you want to use, the citations will placed in the
Unfiled Items collection.
A full overview of databases
and publishers supported by
Zotero is available at:
http://www.zotero.org/translators
The Zotero Translators list includes
Library Catalogs, Databases,
Individual Site Translators and
Metadata Imports.
While in PubMed, open Zotero by clicking
on the Z logo. In the left column, we have
opened the diabetes and developing
countries collection. The additional
citations will be listed in the middle column
of the opened collection.
If you open an individual PubMed entry, you will see
a Save to Zotero (PubMed) option in the drop down
menu of the browser.
By clicking on the option, the Saving to My Library...
message will appear and save the record to the
specific collection that has been opened.
If you are on a page with a list of PubMed
results and select items using the checkbox,
open the Send to drop down menu and click
on Send to ZOTERO using “PubMed” option.
A box will appear with a list of all records from
the PubMed page (next slide).
For the references to be saved,
check the select Items boxes
and click on OK. Options also
include Select All and Delete All.
Exercise 4
• Open Zotero by clicking on the Z logo. In the left column,
open the appropriate collection for your citations.
• Go to PubMed and do a search for articles about:
artemisinin combination or diabetes and developing
countries or a search of your choice
• When you are on the results page, click on the Folder icon
in the address bar:
• Select (check) 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/collection.
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
• 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 (highlight) the items you want to
include in the middle column. To select
multiple items, hold control down and left-click
• 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 (Vancouver)
• 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 Vancouver citation style
and RTF as format. This can be
saved as a Word .doc
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 installing the plugin and clicking on Zotero, 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).
In Firefox, this Software
Installation query may
appear. If so, click on
Install Now.
In MS Word, click on ZOTERO
in the toolbar. This will display
the Zotero Plugin.
The key Zotero options
are listed on this page.
• Zotero Add Citation/Edit Citation
• Zotero Insert Bibliography/Edit Bibliography
• Zotero Set Documents Preferences
(to change the style)
To add a reference ( footnote), click
on the Zotero Add/Edit Citation icon.
If this is the first citation to be
added, the Document Preferences
window will open. Choose the
bibliographic format you want to use
and click on OK – in this case
Vancouver.
The new Z box will appear. Click on the
Check and then Classic View option.
The Add/Edit Citation window will open.
In the Add/Edit Citation window,
highlight the citation you want as
a reference. Add the page # and
click on OK.
We have added 3 Vancouver
style references to this document.
To create a bibliography, click on the Zotero
Insert Bibliography icon. This automatically
adds the bibliography (in the Vancouver
format) to the bottom of the document.
Note: Do not use your word
processor to edit citations. Any
changes automatically will
revert to the original as Zotero
updates your document.
Exercise 7
• Click on Add a plugin for Word or LibreOffice
• Next, click on Word for Windows Plugin (Firefox
extension) and subsequently Install now
• In MS Word or LibreOffice, click on ADD-INS in the
toolbar
• Click on Zotero Insert Citation icon ( ); in Document
Preferences window, choose a bibliographic format; in
the Z box, click on the Classic View option
• In the Add/Edit Citation window, highlight a citation to
add as a reference; include the page # and click on
OK; repeat 2 or 3 times
• Click on the Zotero Create Bibliography icon (
) - to
automatically add the bibliography at the bottom
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 (other options)
• 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/beginnersguide-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
Royal Tropical Institute (KIT) The Netherlands
You Tube Resources
• How to insert Zotero citations and references into a Word
document; explains Add-Ins (Word) uses APA citation style:
• https://www.youtube.com/watch?v=imSxa5MbXrc
• Zotero Overview - covers Chrome, Safari web browsers and
standalone option – including how to sync web and stand
alone (computer) versions; uses Vancouver citation style:
• https://www.youtube.com/watch?v=vNfrv9lD_TM
• Zotero Standalone account – to keep info on your computer:
• https://www.youtube.com/watch?v=H8UTehdF92s
• Zotero Tutorial – covers options of using Chrome and Safari
web browsers:
• https://www.youtube.com/watch?v=7BIrpXYk7M8
Updated 2015 12
Appendix: ZOTERO Standalone 4.0 version
This is the option to download the Zotero Standalone
4.0 for Windows version to your computer’s hard
drive. It can be synced with your library in the
Zotero.org version so that changes in one program
automatically are transferred to the other.
After downloaded, click on the Zotero...setup.exe file
From the Existing Zotero Library
Found window, click on yes - to
import settings from the (Firefox)
Zotero.org version and sync the
existing data directory.
Open the Standalone version
by clicking on the icon that, for
this computer, is listed on the
bottom taskbar.
Once again in PubMed, we have
added another citation to our diabetes
AND developing countries collection –
using the Standalone version.
The Suboptimal... citation has
been added to the collection
in the Standalone version.
Data Syncing of Zotero Libraries
Data Syncing accessed 10 December 2015 https://www.zotero.org/support/sync
Simultaneously, the
Suboptimal... citation has
been added to the collection
in the Zotero.org library.
Standalone Exercise
• Go to the website: www.zotero.org
• Click on the Zotero 4.0 for Windows (Standalone)
• Then click on Yes for Zotero_setup.exe file and Yes
to …import settings from Zotero for Firefox and…
• After installation, click on the Windows version
icon (
)
• Open PubMed, complete a search and save several
citations to your library/collection in the Windows
version
• Open the original Firefox (cloud) version (
) and
confirm that the new citations have been added