Week 3 - Reference Management with Zotero

Introduction

We are using the Zotero reference manager to organize and collaborate on our reference libraries.

Prerequisites

We assume that you have:

1. Completed Assignment 1 & 2 of this course. If you have not, follow the instructions here:

• Assignment 1: https://rbtl-fs22.github.io/website/am-01-hello-github.html
• Assignment 2: https://rbtl-fs22.github.io/website/am-02-hello-rstudio.html

Learning Objectives

In this unit, you will learn to:

1. Create a Zotero Account
2. Add references to Zotero using the Zotero Connector browser add-on
3. Setup a common citekey
4. Use the autopin functionality to update citekeys

Terminology

Open Source

• Open Data Handbook Glossary http://opendatahandbook.org/glossary/en/terms/open-source/
• FORRT (Framework for Open and Reproducible Research Training) Glossary: https://forrt.org/glossary/open-source-software/
• Open Source Inititiative Definition: https://opensource.org/osd

Tasks

1. Setup Zotero Account

1. Open https://www.zotero.org/user/login/
2. Click on “Register for a free account”
3. Chose username, email, and password
4. Click “Register”
5. Open your email and verify your account

2. Join GHE Group Library

1. Login into Zotero: https://www.zotero.org/user/login/
2. Open GHE Group Library: https://www.zotero.org/groups/4609540/rbtl
3. Click on “Join” button
4. Wait for group admin to confirm your membership or contact Lars if you require immediate access

3. Install Zotero Desktop Client

1. Open https://www.zotero.org/download/
2. Download Zotero for your operating system
3. Install Zotero

4. Watch the Video and setup Zotero Preferences

The following video provides instruction to:

1. Install Zotero Connector for the Firefox browser: https://www.zotero.org/
2. Add references:

• https://www.tandfonline.com/doi/full/10.1080/00031305.2017.1375989
• https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005510

2. Install Better BibTeX for Zotero Add-on: https://retorque.re/zotero-better-bibtex/installation/
3. Edit the Zotero CiteKey preferences to the following:

[auth:lower][year][veryshorttitle1_0:lower]

4. Change setting for CityKey autoping delay, also listed here:
   • Open Zotero
   • Open Zotero Preferences
   • Click “Advanced” tab
   • At the bottom of the window under “Advanced Configuration”, click: “Config Editor”
   • Click “I accept the risk!”
   • In the search bar, search for “autopin”
   • Double click into the field under “Value”
   • In the new windows with the title “Enter integer value” change value from 0 to 2
   • Click “OK”

Video

Acknowledgements

The settings that are used in these instructions are inspired by Cortex Futura: How to install Zotero, BetterBibTex and Zotfile.