Putting the Articles in Their Place!

Organize Scientific Literature with Reference Management Software

Colton Baumler

ccbaumler@ucdavis.edu

University of California, Davis

Bryshal Moore

brymoore@ucdavis.edu

University of California, Davis

Wednesday, the 5^th of February, 2025

Overview

Backward design for teaching - “What do you want the audience to take away?”

• This is where you go from surviving to thriving!

• Basics of reference management software

  • Understand the basics of reference management software
  • How to set up zotero for best usage
  • explore functionality of zotero
    • ResearchRabbit
  • Techniques I like think work with zotero

• Background

• Install & Setup

• Suggested Usage

• Techniques for Success

Background

• Reference management software
• Needs of the scholar
• Zotero and others

Reference Management Software Lead to Thriving Scholars

Background

• What is RMS?
  • Database of bibliographic records
  • Creator of bibliographic citations
  • Document and knowledge management
    • Collection structure
    • Tags
    • Notetaking

What influences choice?

• Campus educators (library, dept, etc.)
• Teachers and Colleagues
• But, Overall? Exposure!

Scholars Want the Easiest Tool for Reference Management

Background

User-defined important parameters for RMS. Nitsos et al., 2022, p. 105

Scholar needs?

1. Easy
2. Free
3. Friendly

Zotero is Free, Open-source, Community-driven Software

Background

Participant’s ratings of RMS. Cai et al., 2021, p. 68

Zotero [zoh-TAIR-oh] is a free, easy-to-use tool to help you collect, organize, cite, and share your research sources. - Zotero’s quick start guide

Install & Setup

• Download Zotero
• Optimize Zotero Storage
• Extend Zotero for Knowledge Management

Benefits of a web account

Install & Setup

Benefits

• Free 300 mb storage

Benefits of a web account

Install & Setup

Benefits

• Free 300 mb storage

• Access library anywhere with internet
• Syncing and backup across all devices
• Join shared collections with Zotero groups

Create a web account

Install & Setup

1. Go to zotero.org

Create a web account

Install & Setup

1. Go to zotero.org
2. Click Log In

Create a web account

Install & Setup

1. Go to zotero.org
2. Click Log In
3. Click Register for a free account

Create a web account

Install & Setup

1. Go to zotero.org
2. Click Log In
3. Click Register for a free account
4. Fill out the info

Create a web account

Install & Setup

1. Go to zotero.org
2. Click Log In
3. Click Register for a free account
4. Fill out the info
5. Click Register

Download Zotero for your Operating System

Install & Setup

At zotero.org/download

Details

• Mac
• Windows
• Linux
• Chromebook
• Automatically updates

Zotero Connector in browser simplifies storing articles

Install & Setup

https://forums.zotero.org/discussion/76073/solved-zotero-connector-shortcut-conflict-with-firefox

At zotero.org/download

Details

• Firefox (Recommended)
• Chrome
• Edge
• Safari

Optionally download the app

Install & Setup

• Benefits
  • Portability
  • interoperability
  • Gathering and managing on the go
    • Share 🢖 Zotero app

Click your operating system below:

Downloading plugins to extend Zotero’s abilities!

Install & Setup

• Download the .xpi file for the version you want
  • For Firefox, right-click and Save Link As...
    • OR! Set the Boolean for browser.altClickSave to true at about:config

• Actions and Tags
  • Latest Release

• ZotMoov
  • Latest Release

Install plugins to complete Zotero’s extenstion

Install & Setup

1. Open Zotero

Install plugins to complete Zotero’s extenstion

Install & Setup

1. Open Zotero
2. Select Tools 🢖 Plugins

Install plugins to complete Zotero’s extenstion

Install & Setup

1. Open Zotero
2. Select Tools 🢖 Plugins
3. Select the gear (⚙️) in the top-right corner

Install plugins to complete Zotero’s extenstion

Install & Setup

1. Open Zotero
2. Select Tools 🢖 Plugins
3. Select the gear (⚙️) in the top-right corner
4. Choose Install Plugins From File…

Install plugins to complete Zotero’s extenstion

Install & Setup

1. Open Zotero
2. Select Tools 🢖 Plugins
3. Select the gear (⚙️) in the top-right corner
4. Choose Install Plugins From File…
5. Choose .xpi files to install
6. Select Open
7. Select Install
8. Restart Zotero

Take a few minutes to make sure everything is set up

05:00

Configure Zotero for well-organized storage

Install & Setup

https://forums.zotero.org/discussion/83262/zotfile-move-web-snapshot-web-snapshot-and-cloud-storage https://github.com/jlegewie/zotfile/issues/566 https://ikashnitsky.phd/2019/zotero/ https://ikos-dighum.github.io/contents/betterbibtex/markdown_zotero.html

1. Go to Edit 🢖 Preferences

   • For MacOS, it is Zotero 🢖 Preferences (?)

2. Under General 🢖 File Handling

3. Under General 🢖 File Renaming

Backing up your storage to the web

Install & Setup

3. Under Sync 🢖 Data syncing & File syncing link your web account

4. Under Advanced 🢖 Files and Folders set directories for data and storage

ZotMoov allows automated attachment management!

Install & Setup

10:00

1. Directory to Move/Copy Files To should be your library directory
2. File Behavior leave as Move
3. Set up your directory structure:
   • Nested 🢖{/%y}{/%F}
     for ~/Year/First_Author
     (e.g. ~/2014/ZutJ)
   • Flattened 🢖 /{%y}_{%a}
     for ~/Year_AuthorLastName
     (e.g. ~/2014_Zut)

Zotero can become a personal web archive

Install & Setup

1. Under General 🢖 File Handling

An Example

Migrating to Zotero is mostly painless

Install & Setup

Follow the instructions for any popular tool

You can also import from other tools, such as Reference Manager, RefWorks, Papers, Google Scholar Library, ReadCube, etc., by exporting to a standardized reference format, such as RIS, BibTeX, or CSL JSON, and then importing into Zotero by clicking File → “Import…” and choose “A file”.

Suggested Usage

• Organizing in multiple ways
• Efficiently using Zotero
• AI extensions

A simple, standard directory structure is easy to organize

Suggested Usage

• PARA
  • Projects
    • Short-term efforts
  • Areas
    • Long-term efforts
  • Resources
    • Topics of interest
  • Archives
    • Inactive items from the other categories

A simple, standard directory structure is easy to organize

Suggested Usage

• PARA
  • Projects
    • Short-term efforts
  • Areas
    • Long-term efforts
  • Resources
    • Topics of interest
  • Archives
    • Inactive items from the other categories

Many avenues are available for finding you documents

Suggested Usage

To gather attachments:

• Base Zotero
  • unpaywall
  • retraction watch
• Zotero Connector
  • Database query 🢖 Click 📁
  • Load article or webpage 🢖 Left or Right click item icon

• Addons
  • SciHub
  • This issue for Action tags
• Bypass paywalls
  • archive.today
  • Medium articles
  • Scholar subreddit

05:00

Including headers can increase note organization

Suggested Usage

Including the Notes column for quick reference:

• Right-click column headers in any collection
• Check Notes

Quick example of note taking and importing into text editor:

• Open pdf in Zotero
• Create annotations (Alt+1 & Alt+3)
• Right-click item and Add Note from Annotations
• Open text editor
• Import note

Tags are incredible for organizing with visual aids!

Suggested Usage

Use tags to mark all read and unread items:

1. Add ⭕ to an item in the Tags panel.
2. In the lower left panel, right click the tag 🢖 Assign Color...
3. Select a color and Set color
4. Select all items and drop into the tag

For automatic tagging, install the Actions and Tags addon

For increased resolution create a Folksonomy, a thesaurus of tags

Suggested Usage

Why?

• Individuals or groups will quickly find and re-find sources
• Metadata is shared in groups
  • Offers guidance to beginners

How?

• Think and create some keywords that capture the text contents
• Skim abstracts and papers for keywords
• Use bibliometrics or LLMs:
  • Create a folksonomy, or a thesaurus of tags, for [topics] studies.

Auto-Curate your library through saved searches

Suggested Usage

A final organizational tool within Zotero is the saved searched. By creating curated searches new items will auto populate by well-defined rules set by the user. These saved searches allow a user to find the new items in both their Unfiled collection and their saved searches. All to allow the user more focused options when beginning their reading or writing tasks.

• Start an advanced search:
  • Click the 🔍
  • Click Edit 🢖 Advanced Search
  • Ctrl+Shift+F
• Define an area of continued interest
• Using keywords in All fields, rapidly tag groups of items

05:00

Citing and bibliographies are simplified

Suggested Usage

Paste the citations: Ctrl+Shift+C a Zotero item/s you have selected 🢖 Ctrl+v in text editor

• Google Docs for collabratory documents
  • Open google doc: Open a google doc in the google drive you would like to sync to your Zotero library.
  • Link account: Integrate your google account with Zotero by clicking Z in the toolbar.
    • Authenticate the Google account used to edit the document
• Microsoft Word for local documents
  • Open Word Doc: Open a word document…
  • Done?: There is now a Zotero tab in you document linked to your library!
• Libre Office for local documents
  • Open Libre Writer: Open a writer document…
  • Done?: There is now a Zotero toolbar in you document linked to your library!

Extend your capabilities with addons and external tools

Suggested Usage

Additional addons:

• References
• Scite
• DOI Manager
• Better Notes
• Translate
• An AI Assistant?

Integrated external tools:

• Research Rabbit

External tools:

• semantic scholar
• connected papers
• elicit
• ChatGPT

Techniques for Success

• Achievable Goals
• Boredom

Achievable goals lead to accomplishments

Techniques for Success

%%{init: {
  "theme": "base",
    'themeVariables': {
      'lineColor': 'blue'
    }
}}%%

flowchart TD;
    A[End of the day] ==> B[List 3-6 tasks for tomorrow];
    B ==> C[Order list by priority];
    C ==> D["Pick up at the first item
    the following day"];
    D ==> E[Finish item on list?] ==> G[Move down list!];
    D ==> F[Need a change?] ==> G;

Achievable goals?

• Atomized tasks
  • Focus a task until it is a single operation
  • Doesn’t feel comfortable? The task is still too large
• Monotropism
  • Be intentional with you tasks
  • Reach a flow state in knowledge work

Boredom can lead to creative progress

Technqiues for Success

Ennui/Tedium Slow thought, Processing ideas

• Eliminate distractions
  • Boredom or writing
  • Sit in the arboretum
• Set regular scheduled limits
  • 400 words before editing
  • 3-6 hours before task switching

Summary

Acknowledgments

“I have always imagined that Paradise will be a kind of library.”
Jorge Luis Borges

• C. Titus Brown
• Pamela Reynolds
• Bryshal Moore
• Luiz Irber
• The DataLab
• Professors For The Future
• NSF GRFP
• IMSD

Supplementary

Sync attachments across computers with google drive

Install & Setup - Supp.

1. Download and install Drive for Desktop
2. Skip everything
3. Go to your zotero-library directory
4. Right-click 🢖 Sync or Backup this folder
5. Only check Sync with Google Drive
   • Should now be synced under Computers in google drive
6. In secondary computer,
   1. Download, install, and sync Drive for Desktop
   2. Allow Offline access to zotero-library for local storage
   3. Repeat the Install & Setup section of this presentation to create the same Zotero system on this new computer - BUT! Replace the zotero-library path with the Google Drive zotero-library path (Slide: Zotfile is for automated attachment management, Step 2)

Fixing file locations quickly

Install & Setup - Supp.

zotfile preferences for html

Zotero can also function as a personal web archive. Storing the html files for the websites that are useful for reviewing.

https://github.com/jlegewie/zotfile/issues/566

However, websnap shots have an issue pending in the github repository. They do not automatically rename and move

Simple manual fix until this issue is fixed in an update is to

If your attachments are not all being moved by ZotMoov:

1. Go to My Library
2. Organize by Attachments 📎
3. Click on the webpage icon to the left of the title
4. Select all items (Ctrl+A)
5. Right click 🢖 Manage attachments 🢖 Rename and Move

Better BibTeX supports markdown bibliographies

Install & Setup - Supp.

Better BibTeX Documentation

1. Select Edit 🢖 Preferences
2. Under Better BibTeX 🢖 Open Better BibTeX preferences...
3. Set Citation key formula
   • I suggest auth.lower + year + shorttitle(3,3) + journal.lower.abbr
4. When citing, add @ before the citation key per item cited.