1. Reference Management Software Tools Zotero - Open Source (Module 12)
This work is licensed under a Creative Commons Attribution 4.0 International License
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Managing References

2. 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
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3. 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
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Managing References 3

4. Use a reference management tool!
article
book
conference paper
Your article
citations
reference list/bibliography
Zotero
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Managing References 4

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.
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6. Zotero is a free (open source) reference management tool that
recognizes bibliographic information on books, journal articles, and other resources from websites and databases and extracts metadata from these sources.
stores related citations, PDFs, files, images, and links in your library
creates a citations and bibliographies in Word or OpenOffice documents
publishes shared libraries for your organization, class, or research group
Is available for Mac, Windows & Linux operating systems
To download and install, go to:
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7. Downloading Zotero
Go to the Zotero website at and click on the red Download Now button.
Note: previous modules suggest using Zotero with Firefox but this is not necessary with the 5.0 version.
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Managing References

8. Click on Zotero 5. 0 for Windows Download
Click on Zotero 5.0 for Windows Download. Note the links to options for Other platforms. At some point, you also can Install (Chrome) Connector.
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9. A message similar to this may appear. Click on Install anyway.
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10. Once the software is downloaded, the following slides will appear
Once the software is downloaded, the following slides will appear. Click on Next, Next, Install and Finish.
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11. 30 October 2017
Managing References

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14. This message confirms that You installed Zotero
This message confirms that You installed Zotero. Also available is the link to Install the Zotero Connector for Chrome.
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15. Note: the Zotero Connector extension that automatically senses content as you browse the web and allows you to save it to Zotero with a single click.
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16. Click on the Z in the taskbar; the program with 3 columns will be displayed. The data was transferred from the Zotero 4.0 software that was previously loaded on this laptop.
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17. Exercise 1 Go to the website: www.zotero.org
Click on Zotero 5.0 for Windows
Then click on Install
Once installed, click on the in the taskbar
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18. Zotero Display Overview
While in PubMed (or online), open Zotero by clicking on the Z in the toolbar on the bottom of the computer screen.
Note – you may need to adjust the size of the Zotero and web-browser displays to have the format shown on the slide.
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19. The middle column displays items contained within the selected library
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
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20. Note that in the Tools option, you can Install Browser Connector if not already completed.
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21. In My Library (left column), now opened the diabetes and developing countries collection. The additional citations will be listed in the middle column of the opened collection.
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.
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22. Exercise 2 Click on the Z logo in the toolbar and 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.
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23. 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)
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24. 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 Book.
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.
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25. Now displayed is the More drop down menu for adding material manually
Now displayed is the More drop down menu for adding material manually. Note the extensive list of types of material that can be added.
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26. Exercise 3
In Zotero, click on the New item icon ( ) in the middle column.
Select Book
Enter the 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)
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27. Another way to add a new item is by clicking on the Add Item by Identifier option of Zotero. Enter an ISBN, DOI or PMID – PubMed ID. Zotero will look up the information and import it into your library/collection.
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28. By clicking on the magnifying glass, the Advanced Search option now will be opened.
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29. In the Advanced Search option, you can search for specific titles in My Library. Note the search limit options,
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30. Now completed is a PubMed search
Now completed is a PubMed search. The following slides will show how to move citations to the a Collection in My Library.
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31. Note: your specific collection must be highlighted.
If you open an individual PubMed entry, you will see a Save to Zotero (PubMed) option in the drop down menu of the browser. Click on this option.
Note: your specific collection must be highlighted.
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32. 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. Use Control/right click - to check multiple boxes.
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33. Note the message that the citations are ‘Saving to
Note the message that the citations are ‘Saving to... Diabetes and developing country’ collection.
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34. The citations now are listed in the middle column of Zotero.
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35. Exercise 4
Open Zotero by clicking on the Z logo in the taskbar. In the left column, open the 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 Send to Zotero icon in the address bar:
Select (highlight) some articles to import into Zotero and click on OK
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36. To import citations for webpages into your collection, open the Send to drop down menu and click on Save to Zotero as Web Page.
Information about the current webpage will automatically be saved. You can edit the information by clicking on the fields in the right column.
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38. Exercise 5
Go to the World Health Organization website or a website of interest to you.
When you are in the website, click on the Folder icon in the address bar.
Click on Save to Zotero as Web Page.
Look at your Collection to confirm that the website url has been added.
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39. Attaching files to items
In Zotero, files can be attached to an item. To add attachments to items, click on the paperclip button.
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40. 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.
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41. To create a Zotero bibliography, first highlight the citations that will be the citations. On the keypad, hold control down and click on mouse or touchpad on the individual citations (middle column).
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42. Next, right-click on the mouse or touchpad
Next, right-click on the mouse or touchpad. In the drop down menu, choose the option Create Bibliography from Selected Items, a new dialog box will appear.
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43. Choose the Format (RTF or HTML) to save your document and click on OK.
In the new dialog box, choose the Citation Style you would like to use (Vancouver).
Choose the Format (RTF or HTML) to save your document and click on OK.
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44. Save the bibliography’s file (diabetes & dev Ctires
Save the bibliography’s file (diabetes & dev Ctires.rtf) to the desktop.
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45. This is the example of a Zotero bibliography that was created using the Vancouver citation style in the .rtf format and automatically displayed in MS Word. This can be saved as a Word .doc
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46. Exercise 6
In Zotero, Select (check boxes) the items you have imported from PubMed in the middle column. Hold control and 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
The document will open in MS Word
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47. Word Processor Integration
Zotero's Word and OpenOffice plugins allow users to insert citations directly from their word processing software.
With Zotero version 5.0, the plugin is automatically linked to your Word or OpenOffice version; see toolbar:
Click on ZOTERO and you will see this row of icons in your Microsoft Word toolbar:
These five buttons allow you to manage references and bibliographies in your Microsoft Word documents.
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48. Zotero Add Citation/Edit Citation
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)
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49. 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.
To add a citation (footnote), put the curser at the location in the text document where the citation will be placed and click on the Zotero Add/Edit Citation icon.
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50. The new Z box will appear. Click on the Classic View option
The new Z box will appear. Click on the Classic View option. The Add/Edit Citation window will open.
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51. In the subsequent Add/Edit Citation window, highlight the citation you want as a reference. Add the page # and click on OK.
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52. Add several Citations to the document
Add several Citations to the document. Make sure you move the curser to the point in the document where the additional citations will be.
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53. We have added 3 Vancouver style references to this document.
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54. To create a bibliography, click on the Add/Edit Bibliography icon
To create a bibliography, click on the Add/Edit 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.
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55. Now opened is the Document Preference option
Now opened is the Document Preference option. You can change the Citation Style by clicking on the new format.
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56. Exercise 7 In MS Word or LibreOffice, click on ZOTERO 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
Place your curser at the bottom of the text and click on the Zotero Create Bibliography icon to add the bibliography after the text
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57. 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: (next slide)
Visit the Style Repository and click the “[Install]” link next to the style you wish to install.
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58. Zotero Citation Style Repository
Click on the “[Install]” link next to the style you wish to install.
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59. 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:
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60. Other Zotero tools
From the initial Zotero webpage ( now displayed is the Get Involved subpage with numerous options for participating in the development of this software.
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61. The Zotero Groups is another useful option to view.
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62. Displayed is the table of contents of the Documentation page
Displayed is the table of contents of the Documentation page. Note that the files are being updated for Zotero 5.0 version (October 2017).
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63. This page highlights some of the Tutorials available from the Documentation page.
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