Zotero training session for PhD students - February 2017

1. How to improve my
reference management
with Zotero
February 2017
caroline.peron@univ-amu.fr

2. What is a reference manager software ?
Essential for scholarly reading and writing.
All your bibliographic references are gathered in one database.
A reference manager software can :
- import references from online bibliographic databases (Web of
science, PubMed…)
- share references between different computers and/or users
- store scholarly references on your computer
- create a bibliography on a word processor
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3. How to choose my reference manager software ?
Many choices :
Selection criteria :
- Cost : free to use or personal/institutional license ?
- User interface : easy to learn/ to use ?
- Web storage space : online backup of your references
- Reference management (organization of references, citation
plugin for Word/Open office…)
- Metadata extraction technology (extraction of DOIs, embedded
metadata from PDFs)
- Collaboration (private/public groups, social network)
- Technical support (user forum)
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4. How to choose my reference manager software ?
M. Fenner, K. Scheliga, Reference
Management, Opening science,
http://book.openingscience.org/tools/
reference_management.html ;
http://www.hiig.de/en/reference-
management/
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5. Interesting features of Zotero
• Free and open source (Firefox plugin), easy to use.
• Automatic capture of citation information from web pages.
• Wide variety of import/export options.
• Formated citation export (style list).
• Integration with Microsoft Word and Libre Office.
• Storage of PDFs, links, web pages.
• Advanced search tools (fast search through your references).
• Financed by well known institution (Roy Rosenzweig Center for
History and New Media > George Mason University)
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6. Install Zotero
Use an updated version of Firefox and don’t forget the Word plugin.
Allow the software installation by clicking on « Install now »
http://www.zotero.org/download/
Zotero is successfully installed :
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7. Zotero Standalone
Zotero Standalone runs as a separate application and plugs
into your browser (Google Chrome, Safari).
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8. Zotero 5.0 Beta
Zotero 5.0 includes two major new features, My Publications and
Feeds:
- My publications : it allows you to easily build a list of works —
articles, papers, books, etc. — that you've created and share them
on your profile page on zotero.org.
If you attach files, those files will be made publicly available to
download under a license you specify.
- Feeds : Feeds support allows you to subscribe to RSS or Atom
feeds — such as those made available by academic journals —
from within Zotero. Feeds show up as libraries in Zotero's left
pane, and feed entries are displayed like other items in the center
pane.
Don't try the beta if you're in the middle of a project or would
have trouble restoring your database from a backup if you ran
into problems.
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9. Zotero interface
Toolbar
Files and
tags list
References
Details on the
selected
reference
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10. First step
How to integrate and organize your references
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11. Customize Zotero via the preferences window
Adjust appearance and set miscellaneous
features.
Set your username, password and (if
desired) WebDAV server for syncing
Turn full-text indexing of PDFs on and off
and see relevant statistics.
Specify how bibliographies are generated
Add and remove citation styles
Configure proxy server settings
(not available in Zotero Standalone)
Configure keyboard shortcuts for Zotero
Storage location, database integrity

12. Toolbar
• Add citations to Zotero library :
New citation, added manually
From its identifier (ISBN, DOI, PMID)
From a compatible site or database (Google Scholar, Web of
Science)
- Add attachments to a reference
- Import reference files
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13. Importing citations from compatible databases
and sites
Compatible sites list : http://www.zotero.org/translators/
A folder icon appears next to the zotero icon. Click on it to
import references.
Example : Google Scholar
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14. Importing citations from compatible databases
and sites
Ex: Web of Science, Science Direct, ACS, RSC, Wiley, PubMed, OSA
Publishing, APS, Google Scholar, Sudoc or Aix-Marseille university
catalog…
On a publisher site, Zotero will import the reference + full text
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15. Importing citations from non compatible
databases and sites
Export your citations and save them as a RIS or BibTeX file on your
Desk. (If needed, import this file with the Action icon
Ex: SciFinder, Techniques de l’ingénieur…

16. Importing citations from non compatible
databases and sites
Ex : Techniques de l’ingénieur, import a reference file (format RIS or
BibTeX format), then download it via the Actions icon

17. Creating citations manually
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18. Creating citations from webpages
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19. Creating citations from an identifier
Click on this Identifier icon to create citation from an identifier :
ISBN (13 numbers), DOI, or PubMed ID.
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20. Importing reference by retrieving PDF metadata
Drag your PDF into your Zotero library :
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21. Importing reference by retrieving PDF metadata
Right click on the selected PDF, « Retrieve metadata for the PDF’s »
and install a plugin the first time :
If Zotero can find the PDF in Google Scholar, it creates a new library
item for the paper, downloads the citation information and
attaches the original PDF to the new item.
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22. Creating notes and attachments
To enter notes, click on New Note icon :
To create a note from a reference : click on « Add Child Note »
You can attach files to individual citations in your library, using the
New Child Attachments icon :
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23. Creating note from a web page
Highlight the text that you would like to cite
Right-click on the text and click on « create Zotero Item and Note
from Selection »
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24. Adding note and highlighting PDFs
Zotero doesn’t propose that feature.
You have to use another PDF reader than Acrobat :
- PDF X-Change Viewer for Windows (http://pdf-xchange-
viewer.softonic.fr/) or Nitro PDF reader
(http://www.nitroreader.com/fr/)
- Skim for Mac (http://skim-app.sourceforge.net/)
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25. Organize your Zotero library
In the toolbar, you can choose how to classify your references
(Author, publication date...).
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26. Organize your Zotero library
« My library »
Create a new collection/folder
Drag and drop the collections to create a file tree :
Zotero detects duplicates :
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27. Search for citations in your Zotero library
Quick searching
Advanced searching :
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28. Search for citations with tags
Click on a tag to see items with that specific tag
Search by
selected tag
Tags of the selected
reference (created by
you or downloaded
automatically with
records from
databases)
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29. Search for citations with tags
To assign a color to a tag, right-click the tag in the Tag
Selector (control-click on OS X), and select “Assign
Color…”. Up to six tags can be assigned colors, so you
can highlight important “to read” articles that you would
like to find quickly at a glance.
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30. Add relationships
Create a link between one item and another by clinking on the
« Related » tab :
2 related references
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31. Delete citations
Right click on the selected item. Choose « Delete selected item from
library ».
This deleted item will be stored in the « Waste basket »
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32. Second step
How to create a bibliography and share your references
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33. Cite while you write
You can insert a citation very easily by dragging and droping your
citation :
Citation style can be set up by clicking on the « Actions » icon .
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34. Using Zotero with Word
• Plug-in Word/Open Office :
http://www.zotero.org/support/word_processor_plugin_installation
( Zotero icons are available in the « Adds-in » tab in Word 2007,
2010…)
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35. Using Zotero with Word
The 1st time you insert a citation (using this icon « Add/Edit
citation » ) , you will have to choose a citation style.
Choose citation styles in « Zotero Style repository » (8049 styles
January 2016): http://www.zotero.org/styles
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36. Using Zotero with Word
• Setting up your Cite preferences
The default option when making a selection to cite a reference :
"Classic View" is not the default option when you download Zotero, but it is a
useful option to set up as your preferences:
-Click on the Actions (gear) menu.
-Select Preferences on your drop down menu.
-Select "Cite" in your Preferences box.
-Check the "Classic Add Citation Dialog" option.
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37. Using Zotero with Word
Add / Edit citation (If you edit a citation, you have to place the
cursor inside the relevant citation before pressing this icon)
Insert a bibliography
Edit a bibliography (Ex: add a reference in the bibliography)
Refresh : If you have made changes to your collection, once
you inserted a citation or created a bibliography, click Zotero
Refresh. This will update your references in your document.
Remove Zotero field codes from the document (prevents any
further automatic updates of the citations and bibliographies.)
Change the citation style
http://www.zotero.org/support/word_processor_plugin_usage
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38. Using Zotero with LaTeX
Imports/export on BibTeX :
- Right-click on the selected reference.
- Zotero generates types, fields…
MIT and EPFL guides to create bibliographies using
Zotero and LaTeX

39. Using Zotero with LaTeX
Zotero Better Bib(La)TeX enables to :
- Set your own citation keys
- Drag and drop citations in a LaTeX editor
- Have configurable citekey generator and cleaner (de)LaTeXifier
https://www.zotero.org/support/plugins
https://zotplus.github.io/better-bibtex/Citation-Keys.html

40. Zotero’s online syncing
• Zotero's online syncing allows you to access your Zotero library on
any computer with internet access. Each Zotero user is given 300
MB of free Zotero File Storage for attached files.
• 1st step to syncing your Zotero library : create a Zotero account
Then open Zotero's Sync preferences tab and enter your login
information in the Zotero Sync Server section :
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41. Zotero’s online syncing
Your library online :
You can sync manually at any time by clicking the “Sync with Zotero
Server” button.
http://research.library.gsu.edu/content.php?pid=24410&sid=332122
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42. Syncing with Dropbox
With the release of Zotero version 4.0, it is now possible to choose which
directory Zotero uses when you attach links to files. If you use Dropbox
Basic (2GB of free storage), you can now save your citations in Zotero,
attach links to files in a Dropbox folder, and have both synchronize with
every computer you use.
http://libguides.princeton.edu/content.php?pid=31604&sid=3799749
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43. Export your Zotero library
Zotero allows you to export your Zotero library as a Zotero RDF
file to copy your library.
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44. Zotero groups
Zotero groups, enables you to collaborate with project members,
and set up web-based bibliographies for classes you teach.
Share your own work or sources you have discovered with others
who are working in related areas.
Collaborate with colleagues, publicly or privately, on ongoing
research.
Discover other people with similar interests and the sources they
are citing.
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45. Zotero groups
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46. Zotero groups
Private Groups
Only group members and users invited to join the group are able to
see the group’s page.
Private groups are completely hidden from group searches. They are
not shown on members’ public profile pages and will not appear in
search engine results.
Public, Closed Membership
Anyone can view the group page, but the only way to join the group
is by invitation or by requesting an invitation.
If the group has a public library, administrators can choose to show
or hide the entire library or individual collections from non-members.
Public, Open Membership
The group page is public, and anyone who wants to can join
instantly.
If the group has a public library, administrators can choose to show
or hide the entire library or individual collections from non-members.
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47. Export your EndNote library to Zotero
Select “Output Styles” from the Edit menu.
From the list of output styles select RefMan (RIS).
Select “Export” from the File menu.
In the Export window that pops up, choose “Text Only”, select the RIS
output style immediately below “Text Only” in the dialog, and hit
“Save.”
After exporting from EndNote, click on the gear icon in your Zotero
pane and select « Import » from the pull-down menu.
In the file system window that pops up, locate the RIS file you
exported from EndNote and select “Open.” Your references should be
imported into Zotero.
The same basic steps apply to many other reference management
systems.
http://www.zotero.org/support/kb/importing_records_from_endnote
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48. Export a bibliography from Word to Zotero
Use a parser like Wizfolio : http://wizfolio.com/
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49. Useful links
Zotero quick start guide : http://www.zotero.org/support/quick_start_guide
Beginner’s guide to using Zotero (University of British Columbia) :
http://www.slideshare.net/giustinid/beginners-guide-to-zotero
Backing up your Zotero library :
http://libguides.northwestern.edu/content.php?pid=68444&sid=676064
Requesting styles on Zotero forum : https://github.com/citation-style-
language/styles/wiki/Requesting-Styles
Editing style with CSL editor (collaboration between Columbia University
Libraries and Mendeley) :
http://editor.citationstyles.org/about/
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