Complete Guide: Using Zotero with Thetapad for Academic Writing

Why Zotero + Thetapad?

Managing references is one of the most tedious parts of academic writing. You find papers, save them somewhere, then manually format citations when writing.

Zotero handles reference management—collecting, organizing, and formatting citations. Thetapad handles document writing—fast LaTeX compilation with real-time collaboration.

Together, they create a seamless workflow: collect references in Zotero, cite them effortlessly in Thetapad.

Prerequisites

Before we start, ensure you have:

1. Zotero installed (zotero.org)
2. Better BibTeX extension for Zotero
3. Thetapad account (free tier works fine)

Installing Better BibTeX

Better BibTeX is essential for LaTeX users. It provides:

• Automatic .bib file generation
• Customizable citation keys
• Automatic export updates
• Better handling of special characters

To install:

1. Download from retorque.re/zotero-better-bibtex
2. In Zotero: Tools → Add-ons
3. Click the gear icon → Install Add-on From File
4. Select the downloaded .xpi file
5. Restart Zotero

Setting Up the Integration

Step 1: Configure Citation Keys

Better BibTeX generates citation keys for each reference. Configure the format:

1. Edit → Preferences → Better BibTeX
2. Set your citation key format, for example:

   [auth:lower][year]

   This creates keys like smith2024, johnson2023

Other popular formats:

• [auth:lower][year][shorttitle:lower] → smith2024machine
• [auth:lower:alphanum]_[year] → smith_2024

Step 2: Create an Auto-Exporting Library

Set up automatic BibTeX export:

1. In Zotero, select a collection (or your entire library)
2. Right-click → Export Collection
3. Choose "Better BibTeX" format
4. Check "Keep updated"
5. Save as references.bib in your Thetapad project folder

The file now auto-updates whenever you add or modify references.

Step 3: Link to Your Thetapad Project

In your LaTeX document, add the bibliography:

\documentclass{article}
\usepackage[backend=biber,style=authoryear]{biblatex}
\addbibresource{references.bib}
 
\begin{document}
 
Your text here \parencite{smith2024}.
 
\printbibliography
\end{document}

For the simpler BibTeX approach:

\documentclass{article}
\bibliographystyle{plain}
 
\begin{document}
 
Your text here \cite{smith2024}.
 
\bibliography{references}
\end{document}

The Daily Workflow

Adding New References

When you find a paper to cite:

1. In your browser: Click the Zotero browser extension
2. Zotero imports the reference automatically
3. Better BibTeX exports to your .bib file
4. In Thetapad: Use the citation key immediately

Example:

Recent work shows \parencite{newpaper2024} that...

The whole process takes seconds.

Citing References in Thetapad

Common citation commands:

% Parenthetical citation: (Smith, 2024)
\parencite{smith2024}
 
% Textual citation: Smith (2024)
\textcite{smith2024}
 
% Multiple citations: (Smith, 2024; Johnson, 2023)
\parencite{smith2024,johnson2023}
 
% Citation with page numbers: (Smith, 2024, p. 42)
\parencite[p. 42]{smith2024}
 
% Just the year: (2024)
\parencite*{smith2024}

For traditional BibTeX (using natbib):

\usepackage{natbib}
 
\citep{smith2024}      % (Smith, 2024)
\citet{smith2024}      % Smith (2024)
\citep[p. 42]{smith2024}  % (Smith, 2024, p. 42)

Managing the Bibliography File

Your references.bib might look like:

@article{smith2024,
  author = {Smith, John and Johnson, Mary},
  title = {A Comprehensive Study of Machine Learning},
  journal = {Journal of AI Research},
  year = {2024},
  volume = {15},
  pages = {100--125},
  doi = {10.1234/jair.2024.15.100}
}
 
@book{johnson2023,
  author = {Johnson, Mary},
  title = {Introduction to Deep Learning},
  publisher = {Academic Press},
  year = {2023},
  isbn = {978-0-123456-78-9}
}

Better BibTeX handles all the formatting—you never edit this manually.

Advanced Techniques

Project-Specific Libraries

For different projects needing different references:

1. Create a Zotero collection for each project
2. Export each collection to its own .bib file
3. Auto-export keeps each synchronized

thesis/
├── main.tex
├── thesis-refs.bib  ← exported from "Thesis" collection
 
paper-neurips/
├── paper.tex
├── neurips-refs.bib  ← exported from "NeurIPS 2024" collection

Handling Citation Key Conflicts

If two papers have the same author and year:

Better BibTeX automatically creates unique keys:

• smith2024 (first paper)
• smith2024a (second paper)

You can also customize keys manually in Zotero:

1. Right-click reference → Better BibTeX → Pin BibTeX Key
2. Enter your preferred key

Syncing Across Devices

Your Zotero library syncs via Zotero's cloud (free for metadata, paid for file storage).

For the .bib file:

• Store in a synced folder (Dropbox, Google Drive, Git)
• Or use Zotero's auto-export to the same location on each machine

Collaborative Bibliography

For team projects:

Option 1: Shared Zotero Group

1. Create a Zotero group library
2. Invite collaborators
3. Everyone adds references to the shared library
4. One person exports to .bib (or everyone uses same export path)

Option 2: Shared .bib File

1. Each person maintains their own Zotero
2. Export to a shared .bib file (via Git or shared drive)
3. Merge conflicts manually if needed

Troubleshooting

Reference Not Appearing

Symptom: You cite \cite{smith2024} but get [?] or missing reference error.

Solutions:

1. Check the citation key exists in your .bib file
2. Verify the .bib file path in \addbibresource{} or \bibliography{}
3. Run BibTeX/Biber (Thetapad does this automatically)
4. Check for typos in the citation key

Better BibTeX Not Exporting

Symptom: Changes in Zotero don't appear in the .bib file.

Solutions:

1. Verify auto-export is enabled (check "Keep updated" when exporting)
2. Right-click collection → Better BibTeX → Refresh BibTeX Key
3. Check export path is correct
4. Restart Zotero if needed

Special Characters Breaking

Symptom: Names with accents or special characters cause errors.

Solutions: Better BibTeX handles most cases, but if issues persist:

1. In Better BibTeX preferences, check "Export unicode as plain-text LaTeX"
2. Verify your LaTeX document uses \usepackage[utf8]{inputenc}

Duplicate Citation Keys

Symptom: Two references have the same key, causing confusion.

Solutions:

1. Better BibTeX usually handles this automatically (adding a, b, c suffixes)
2. Pin specific keys for important references
3. Use a more specific key format: [auth:lower][year][shorttitle:lower]

Best Practices

1. Use Consistent Citation Keys

Pick a format and stick with it. Recommended:

[auth:lower][year]  →  smith2024

Avoid formats that change when you edit the reference.

2. Keep .bib Files in Your Project

Store the .bib file with your LaTeX source:

my-paper/
├── main.tex
├── references.bib  ← in the same directory
├── figures/

This ensures the project is self-contained.

3. Version Control Your Bibliography

If using Git:

git add references.bib
git commit -m "Add references for methods section"

This tracks changes and allows collaboration.

4. Clean Up Unused References

Before submission, remove unused references:

1. In Zotero, check which references aren't cited
2. Or use tools like checkcites for LaTeX

5. Verify Before Submission

Always check:

• All citations resolve correctly
• Bibliography formats match journal requirements
• No [?] markers in the output

Comparison: Zotero vs Other Reference Managers

| Feature | Zotero | Mendeley | EndNote | |---------|--------|----------|---------| | Price | Free | Free/Paid | Paid | | BibTeX Export | Excellent (with BBT) | Good | Limited | | Auto-sync to .bib | Yes (with BBT) | No | No | | Open Source | Yes | No | No | | Browser Extension | Excellent | Good | Good | | LaTeX Integration | Best | Adequate | Poor |

For LaTeX users, Zotero + Better BibTeX is the gold standard.

Conclusion

The Zotero + Thetapad workflow transforms citation management:

1. Collect references effortlessly with Zotero's browser extension
2. Organize them in Zotero's library
3. Auto-export to BibTeX with Better BibTeX
4. Cite in Thetapad with simple commands
5. Compile and see perfectly formatted citations

No more manual formatting. No more copying between apps. No more citation errors.

Set up once, and every paper you write benefits.

For more citation styles and advanced BibLaTeX configurations, see our comprehensive LaTeX bibliography guide.