Up to speed with Zotero

INTRODUCTION
About

Description
These course notes have been created for EPFL Library's training Up to speed with Zotero - quick start
workshop, in Lausanne, Switzerland. Slides for this training are available on https://go.epfl.ch/ztart2022.

Authors
This training was created and is maintained by the EPFL Library Teaching Team, including:

Mathilde Panes [email protected]

Miriam Petrilli [email protected]

Former members:

Angélique Boschung
Raphaël Grolimund
Caroline Salamin
Noémi Cobolet

Version 2.08
updated on February 20, 2020 (version history)

The latest version of this document is available on gitbook: https://go.epfl.ch/zotnotes

Translation
If you are interested in the french version of these course notes, please check the corresponding repository :
https://go.epfl.ch/zotbook-fr.
License CC BY

This document is available under the following license Creative Commons Paternité 4.0 International.
The source files can be found here https://github.com/epfllibrary/zotero-course.
Feel free to reuse and remix them!

Introduction

Learning objectives
By the end of this workshop, participants will :

1. install Zotero

2. create a Zotero library

3. collect references and metadata from various sources

4. cite and create bibliographies
5. choose a citation style

Program

Time Activity

00:00 Introduction

00:05 Comparing reference management softwares

00:15 Zotero Installation

00:30 Create a Zotero library

00:35 Exercise time (4.1 - 4.3)

00:50 Collect references

01:05 Break

01:20 Exercise time (4.4 - 4.6)

01:30 From Zotero to a word processor (5.1 - 5.3)

 01:40 Citation styles (6.1 - 6.2)
01:50 Questions, evaluation and conclusion

Comparing reference managers

Comparing reference managers

Papers/ReadCub
BibTeX EndNote Mendeley Zotero
e

owned by
owned by
owned by Digital Science &
free license Clarivate free license
Elsevier Research
Analytics
Solutions, Inc.

free of charge 275,- CHF* free of charge $60/year** free of charge

integrated integrated integrated integrated integrated

with with with with with
(Word) Word Word Word Word
(OO/LO***) OO/LO*** OO/LO*** OO/LO*** OO/LO***
LaTeX (LaTeX) (LaTeX) (LaTeX) LaTeX

??? 6,000+ 9'000+ 9'000+ 9'000+

citation citation citation citation citation
styles styles styles styles styles

* student discount: CHF 127.67 (in Switzerland)

** student discount: $36/year *** OO/LO: Open Office / Libre Office

Why a reference manager?

Zotero is a reference manager. When you use a reference manager, the following tasks are (more or less) a
1-click process:

add/import references

create a bibliography
 cite while you write a paper

All these technical tasks should be done by the software, but remember that you are the brain. This means
that you should:

read the documents (:wink)

check if the reference data are correct and complete

sort references
select relevant references to add in the bibliography

It is important to understand that this kind of software is made to manage a bibliography, not several items of
a same document. It's not suitable to keep track of who borrowed what document (e.g. in the lab collection).

Why Zotero?

Zotero is user-friendly and powerful. Most ot the recent reference managers chose a similar interface or
workflow.
Zotero is compatible with a large number of online resources: as of January 2018, more than 500 fully
compatible resources (more than any other reference manager).
It's free. Not only free of charge, but above all it's a free and open source software (no restriction due to the
license agreement). This means that when you will leave EPFL, you will still be able to use it like you did
here.
Zotero has also a large and active community of users. If you need help, you can quickly get an answer to
the issues you face. If you need a feature, its implementation doesn't depend on the developers' willing to do
it: you can ask for it (maybe another user already implemented it) or do it by yourself.
Zotero is modular: additional features can be added and shared through plugins
(https://www.zotero.org/support/plugins).

Finally, and even if it's not covered in this workshop, it's important to know that Zotero is made for
collaborative work, more than any other reference manager. This includes unlimited members and unlimited
items for an unlimited number of group libraries. There are storage space limitations, though.

All the reasons above explain why we choose to focus on Zotero.

INSTALLATION
Installing Zotero

How to install Zotero?

1. Go on https://www.zotero.org/download/
2. Download Zotero 5.0
 3. Run the installation file

You will also need to install the Zotero connector for your browser.

1. Go on https://www.zotero.org/download/

2. Click on the "Install Zotero Connector" button

3. Autorize installation

As of November 2019, the Zotero Connector for Safari is unavailable for download, and existing
installations will stop working if you upgrade to Safari 13 and/or macOS Catalina. Existing installations will
continue to work in Safari 12. The Zotero team is hoping to release a working connector for Safari shortly.
We recommend you install Firefox as an alternative browser.

How to check if the installation worked ?

Zotero should now be installed on your computer. To fully enjoy Zotero, the software should be plugged in
your browser and your word processor (Microsoft Word, OpenOffice Writer, LibreOffice Writer).

1. Check if Zotero is installed by opening the application on your computer

2. Open your browser and check that Zotero appears on the top bar, next to the search bar
3. Open your word processor and check if the Zotero plugin is installed. This plugin is also called "Word
processor". Usually, after installing Zotero, a new tab will appear in your word processor. Depending on
your software, Zotero might alternatively be shown with other "complements".

If the installation of the Word Processor did not work, you can reinstall it from Zotero itself.

1. Open Zotero

2. Go to Edit > Preferences (or Zotero > Preferences on Mac OS)

3. Click on the Cite tab
4. Click on the second tab Word Processor
5. At this stage, you can choose to install or reinstall one word processor or more, according to the number
you have on your computer.

DIG INTO ZOTERO

Creating a Zotero library

Zotero Library
Your Zotero library will contain all the references you add into your library. You can create subsets of your
library by adding "collections".

zotero interface

Collecting references
A reference consists of metadata describing a document and allowing you to easily find the document later.
Zotero structures the metadata you collect about documents. When you cite your documents with Zotero, it
will then generate consistent bibliographies. Zotero also allows you to store digital files along with the
references.

The best is to collect references while you are in the process of looking for information. By that, we mean
that you will be more efficient if you directly collect the metadata while you are on the website / database /
library catalog where you find your documents because you won't need to find the reference a second time
afterwards.

... with Zotero Connector

The Zotero Connector is the plugin that you installed in your browser. This plugin will detect the references
available on the page you are visiting. The quality of the metadata depends on the sources you visit.
Open Zotero and click on the Zotero connector icon in your browser : the reference will be automatically sent
to your Zotero library.

Example : an article from Cytology

... using RIS or BibTeX
Some databases or catalogs can provide you with a downloadable file containing one or more references.
The most common formats for these kind of files are RIS (.ris) or BibTeX (.bib). It is most useful for large
scale exports.

Example : here is a sample file to download

... with a unique identifier (DOI, PMID, ISBN).

Documents are often attributed a unique identifier: this helps when you have a copy of this document and
you want to add the reference to Zotero.

In Zotero, if you click on the magic wand icon in the top bar, a field appears. Type the identifier of the
document. Press enter. A new reference will be added to your library.

Example : the ISBN of a book, DOI of a scientific paper or the PMID of a biomedical paper.

... from a PDF

If you have stored PDFs on your computer without directly adding them in Zotero with their metadata, it's
often possible to obtain comprehensive metadata afterwards.

You need to add the PDF in Zotero, by dragging it from a folder and dropping it in your library. Zotero
automatically searches for metadata and automatically create a reference containing the metadata along
with the PDF file when possible. However, it might be that the PDF you added to your Zotero library is not
machine-readable or is not recognized by Zotero. In that case, no metadata will be retrieved. You can also
retrieve metadata for several PDFs at the same time.

Example : a PDF sent by a colleague

... manually

Sometimes, there is no available metadata encoded in the page you are visiting or the document you have
in your hands is not indexed in a digital catalog. You will need to create or edit the reference yourself.

In Zotero, you can create a new item by clicking on File > New Item or on the green circle with a plus. Either
way, you will need to choose the type of document you want to create a reference for (ie "Book", "Report",
etc.). When you select the type of document, a blank reference appears. You can then fill the fields
according to the document you have in front of you. In all cases, it is best to be exhaustive as possible and to
give as much information as possible.

Example : a report from the Swiss Federal Statistical Office

Retrieve PDFs

In some cases, you might want to store a copy of the full text associated with the bibliographic reference. It is
possible to retrieve and add full text PDFs in two ways. 1. While adding a bibliographic reference from the
browser. 2. Later on, doing a right-click on a reference (or a batch of references) and clicking on "Find
available PDF"
exercises

exercise 4.1: Collect references

Add 5 references in your Zotero library. Try adding references of various doctypes:

1. book

2. paper

3. conference paper

4. Wikimedia Commons image

5. thesis

exercise 4.2 : Search for a reference

Find at least two ways of searching a reference in your library.
Try the advanced search and save the result.
The collection created from that search is dynamic: every new reference matching the query you used in the
avdanced search will be added automatically in this collection.

exercise 4.3 : Check for the full text version of the document
Select a batch of references with no attachments. References with attachments have a blue dot on the side.

Use the "Find available PDFs" feature to check PDFs availability. Zotero will import full text version of the
document when available.

Answers and personal notes

exercises

Your Zotero Library is organized in columns: first colum is usually the arborescence of your files /
collections.

You can create as many files / collections and subcollections as you want. Each item / reference will appear
two times: first occurence is in your Library, and second occurence is in the collection if you put it in one of
your collections.
Items that are not filed are listed in the "Unfiled Items" file.
exercise 4.4 : Create and manage your collections
Create a collection. Put some of your references in this new collection. Click on one of the references and
delete it from the collection, but not from your Library.

Which option should you select?

exercise 4.5 : "Duplicate Items" collection

What is this collection made for?

exercise 4.6: Modify a record

Now that you are familiar with your collections and the list of your items, let's have a look on the record of
each of your item.

Where do you see the metadata of each of your reference?

Depending on the metadata found on the webpage by Zotero, some modifications of a record in your Library
can be necessary. Are the items you just collected correct and complete?

Which are the main fields for the reference of a journal article? And for a thesis, a report, a ?

exercise 4.7: Comment your references

Add insightful comments to your references: Add a note on one item from your Library

Answers and personal notes

From Zotero to the word processor

From Zotero to the word processor

Zotero integrates very well with Microsoft Word and LibreOffice Writer. There are several ways to add
references from a Zotero library in a word processor.

First, both Zotero and the word processor have to be open. Then, to be able to use the interactive features,
you need to have a Zotero button in your word processor. Can you see it? If not, in Zotero, open the
Preferences panel and go to Cite > Word Processors and click on the "reinstall [name of the word processor]
Add-in" button.
Zotero and LaTeX
It's also possible to use Zotero with LaTeX.

With Overleaf

To connect Overleaf with your Zotero library go to "settings" and look for "link to Zotero". Your overleaf
account is now linked to your Zotero library. In your paper, create a new file uploaded from Zotero with the
.bib extension. This file contains your entire Zotero library in bibtex format. For each reference, the first line
is the key you have to use for citing.

Example: \cite{jawahar_viena_2019}

Overleaf and group libraries

A great feature of both Zotero and Overleaf is the ability to work collaboratively. However, synchronising
Zotero group librairies with Overlead requires some extra steps. You will need to:

1. Make your Zotero group library public (Public: Closed Membership / Group Library: Anyone can view,
only members can edit)
2. Find the unique number of your Zotero group library by opening the group via Zotero.org

[add image]

1. Add a .bib file from an external URL with the following URL: https://api.zotero.org/groups/[unique group
id]/items/top?format=bibtex&style=numeric&limit=100

With TexMaker or another LaTeX editor.

Export your references from Zotero in a bibtex file. The file will not be up to date in case if you add, modify or
remove references in Zotero. Use the keys in the same way as previously for citing. For advanced use of
LaTeX within Zotero, BetterBibTex, an independently developped plug-in can be useful

exercises

exercise 5.1: Create a bibliography without citing

Generate a bibliography in your word processor by selecting at least 3 references from Zotero. There are at
least 2 ways to do it.

exercise 5.2: Cite while you write

Insert 3 citations and then create a bibliography

1. Write a few lines about your area of expertise.

 2. In your text, cite at least 3 documents that are saved in Zotero. TIPS: use the Zotero button in your word
processor + you are free to select any citation style.
3. Generate a bibliography

exercise 5.3: Zotero and LaTeX ?

If you use Overleaf, what are the steps to link Overleaf to Zotero ?

If you use LaTeX locally, you can export your Zotero library to use it with your LaTeX source file : what is
the format of the file you need to export from Zotero ?

Answers and personal notes

Citation styles

Citation styles
In this part, you will learn how to change citation styles and how to add new ones.
Citation styles change how citations appears in your texts and the way metadata is displayed when you
create a bibliography.

A citation style applies rules about which metadata to display for each document type as well as how to
format the in-text citation and the reference. These citation styles can be defined by publishers, scientific
societies or individuals, for instance. Theoretically, you could apply the citation rules manually, but Zotero
will be faster and more consistent.

It is possible to modify or create one's own citation style, but we don't cover this topic in this course.

Changing your style... from Zotero

More than 9'000 styles are available for Zotero!
If you want to apply a citation style to bibliographies you directly create from your Zotero library, you need to
select the citation style in Zotero.

1. Open Zotero
2. Go to Edit > Preferences
3. Click on the Cite tab
4. In the newly opened Styles tab, choose the style you want to apply to your bibliography
5. Click on "OK"
Changing your style... in a document
If you want to change the citation style in a document, you need to make the changes in the word processor /
Zotero add-in.

1. Open the document in the word processor

2. Go on the "Zotero" tab
3. Click on "Document Preferences" button

4. Choose the style you want to apply from the preloaded list
5. Click on "OK"

Changes will be applied automatically.

Finding a style suiting your needs

There are so many citation styles available for Zotero, some might suits your needs and look better than
others. If you want to look for another style, you can check the Zotero Style Repository. In this repository you
can search citation styles by title, format and field. For each style, a preview is available. The repository is
also directly searchable from Zotero.

Adding a new style in Zotero

Citations styles can be added in 3 different ways :

1. Directly from a .csl file saved on your computer

2. From the Zotero Style Repository embedded in Zotero
3. From the online Zotero Style Repository

Directly from a .csl file saved on your computer

If you dowloaded a .csl file you can add it to Zotero with the following steps :

1. Open Zotero
2. Go to Edit > Preferences
3. Click on the Cite tab
4. In the newly opened "Styles" tab, click on the + sign, just below the preloaded style list
5. Browse your computer to find the .csl file you want to add

6
 6. Select the .csl file
7. Click on "Open"

The new citation style is added to the list in Zotero and in the word processor.

From the Zotero Style Repository

It is also possible to integrate a style directly from Zotero via the Zotero Style Repository with the following
steps :

1. Open Zotero
2. Go to Edit > Preferences
3. Click on the Cite tab
4. In the newly opened "Styles" tab, click on "Get additional styles", just below the preloaded style list
5. The Zotero Style Repository will open
6. Search for the style you want to add and click on it

The new citation style is added to the list in Zotero and in the word processor.

If you choose to use the online Zotero Style Repository, go to https://zotero.org/styles and skip steps 1-5
above.

exercises

exercise 6.1: Add a new citation style

Your supervisor/publisher requires that you use a citation style called Copernicus.
Copernicus is not listed in the short list! How can you add it to the citation styles list in Zotero?

exercise 6.2: Change the citation style

Finally, you submit your paper to a different journal than the one you first planned. The IEEE style is required
for referencing. Arrrgghh!! What can you do?

Answers and personal notes

THE END (SO FAR...)

Conclusion
This workshop was intended to give you the basics to start working with Zotero.

Advanced Zotero features

There are various Zotero features that were not covered in this workshop, such as :

Setting up your Zotero account to sync your library

Working in groups with Zotero

RSS feeds

Increase storage space using a WebDav-enabled 3rd party platform

How to use annotated PDFs within Zotero

Advanced PDF management with Zotfile

Don't hesitate to ask us if you want explanations about these features.

Support

The EPFL Library Training Team is always keen to support you in your use of Zotero and will also reply to
your questions about citation in general.
Lab-centered workshop or support are also provided on demand.

You can contact us by e-mail: [email protected].

We will answer your question or set an appointment depending on the specificity and complexity of your
request.

References & useful links

References
KARCHER, Sebastian and ZELLE, Rintze, 2015. Mastering Zotero: a user guide for the Zotero reference
manager [online]. 18 November 2017. [Accessed 15 January 2017]. Available from: https://zotero-
manual.github.io/zotero-manual/

KRATOCHVÍL, Jiří, 2017. Comparison of the Accuracy of Bibliographical References Generated for Medical
Citation Styles by EndNote, Mendeley, RefWorks and Zotero. The Journal of Academic Librarianship. 2017.
Vol. 43, no. 1, p. 57–66. DOI 10.1016/j.acalib.2016.09.001

MURACK, Jennie, 2018. LibGuides: Citation Management and Writing Tools: Zotero. [online]. [Accessed 5
December 2018]. Available from: https://libguides.mit.edu/cite-write/zotero

PUCKETT, Jason, 2017. Zotero: a guide for librarians, researchers and educators. 2nd ed. Chicago, Illinois:
ACRL. ISBN 978-0-8389-8931-9.
Useful links
Zotero Forum to get help from the large Zotero community:
https://forums.zotero.org/discussions

Zotero official blog for news from the Zotero team:

https://www.zotero.org/blog/ (2 posts/year)

The "blog francophone" de Zotero for more information:

https://zotero.hypotheses.org/ (in French)

Plugins for Zotero to add features:

https://www.zotero.org/support/plugins

Version history
0.99: initial version (05.01.2018)

1.00: 1st public version (16.01.2018)

2.00: 2nd public version (02.05.2018)

2.01: minor corrections (18.06.2018)

2.02: nitpicking by Caroline (16.10.2018)

2.03: minor updates (05.12.2018)

2.04: minor updates for forthcoming training (21.02.2019)

2.05: some cosmetic updates for forthcoming training (25.09.2019)

2.06: preparing forthcoming training (22.10.2019)

2.07: update for forthcoming training, edit exercises (13.11.2019)

2.08: add instruction for SWITCHdrive usage (22.11.2019)

ADVANCED ZOTERO FEATURES

(BETA CONTENT)
Setting up additional storage

In this second part of the course note, we will describe advanced features.
Enabling unlimited storage as an EPFL member
As of November 2020, the EPFL has an institutional subscription for all EPFL members who use Zotero. To
have access to this storage, you must set your @epfl.ch e-mail address as primary or secondary e-mail in
your Zotero account. If you want to modify the address e-mail of Zotero account, you should go to zotero.org,
log in and click on your name. In the menu under your name, select settings. You will land on your Zotero
profile. Change to 'Account' to land on the page where you will have the ability to modify the e-mail(s) linked
to your account.

Using WebDav storage : how to set SWITCHdrive up

EPFL members and members of universtities and institutions of higher education in Switzerland can use
SWITCHdrive. SWITCHdrive gives 50 GB of space to use as a free cloud storage (to store files, for
instance). However, if you are affiliated with EPFL, you can rely on the unlimited storage described
above

SWITCHdrive can also be used to get more storage for your Zotero library. When you start using Zotero with
an account on zotero.org, you freely get access to 300 MB of storage on Zotero's server.

This space is used to synchronise your libraries on several computers and to provide you with an online
version of your library, accessible via an internet browser.

SWITCHdrive can do the same, except with a much higher storage size !

If you want to benefit from this space, here is how :

1. Register on SWITCHdrive registration page

2. Open Zotero and go to Preferences > Sync

3. From this pane, you can change your synchronisation settings. Make sure data syncing is set up. You
will need to have a Zotero account for this

4. From the same pane, you can choose which file storage to use. Choose "WebDAV", as shown below
5. To make the connection between your Library and SWITCHdrive servers, please define the URL as
shown below

6. Enter your username and password. They are the same you used to create your SWITCHdrive account

7. Verify the link with the server by clicking the dedicated button

Synchronisation is now handled through SWITCHdrive.