Mendeley + Thetapad: Seamless Citation Management

Why Mendeley + Thetapad?

Mendeley is one of the most popular reference managers, with features for:

• Storing and organizing papers
• Annotating PDFs
• Discovering related research
• Collaborating with groups

Combined with Thetapad's LaTeX editing, you get a complete academic writing workflow.

Setting Up the Integration

Step 1: Install Mendeley Desktop

If you haven't already:

1. Download from mendeley.com
2. Install and create account
3. Import your existing references

Step 2: Configure BibTeX Export

Mendeley can auto-export a .bib file:

1. Open Mendeley Desktop
2. Go to Tools → Options (Windows) or Mendeley Desktop → Preferences (Mac)
3. Select the BibTeX tab
4. Enable "Sync library to BibTeX"
5. Choose an export path (e.g., your project folder):

   /path/to/your/project/references.bib

6. Set Citation Key format (recommended: AuthorYear)

Step 3: Link to Your Thetapad Project

In your LaTeX document:

\documentclass{article}
\usepackage[backend=biber,style=authoryear]{biblatex}
\addbibresource{references.bib}  % The exported file
 
\begin{document}
 
As shown by \textcite{smith2024}, this approach works well.
 
Multiple studies support this \parencite{jones2023,brown2022}.
 
\printbibliography
\end{document}

The Daily Workflow

Adding New References

1. Find a paper you want to cite
2. Import to Mendeley:
   • Use the browser extension
   • Drag PDF to Mendeley
   • Add manually
3. Mendeley exports to your .bib file automatically
4. In Thetapad: Use the citation key immediately

Citing in Your Document

% Author (Year) style
\textcite{smith2024}  % Smith (2024)
 
% (Author, Year) style
\parencite{smith2024}  % (Smith, 2024)
 
% Multiple citations
\parencite{smith2024,jones2023}  % (Smith, 2024; Jones, 2023)
 
% With page numbers
\parencite[p. 42]{smith2024}  % (Smith, 2024, p. 42)

Checking Your Bibliography

Your exported references.bib looks like:

@article{smith2024,
  author = {Smith, John and Johnson, Mary},
  title = {A Study of Machine Learning Applications},
  journal = {Journal of AI Research},
  year = {2024},
  volume = {15},
  pages = {100--125},
  doi = {10.1234/example}
}

Mendeley maintains this automatically as you add references.

Optimizing the Workflow

Customizing Citation Keys

Mendeley generates citation keys automatically. To customize:

1. In Preferences → BibTeX
2. Set Document ID to your preferred format:
   • AuthorYear → smith2024
   • AuthorTitleYear → smithMachineLearning2024
   • AuthorYearTitle → smith2024MachineLearning

Organizing References

Create Mendeley folders for different projects:

• Export only the relevant folder to each project's .bib
• Keep your main library separate from project-specific files

Handling Special Characters

Mendeley handles most special characters, but watch for:

• Accented names (proper UTF-8 encoding)
• Math symbols in titles (may need escaping)
• Unusual punctuation

If issues arise, edit the entry in Mendeley and re-export.

Collaboration with Mendeley Groups

Shared Bibliography for Team Projects

1. Create a Mendeley Group
2. Add team members
3. Everyone adds references to the shared library
4. Export the group library to a shared .bib file

Syncing the Exported File

For team access to the .bib:

Option A: Shared folder (Dropbox/OneDrive)

• Export to synced folder
• Everyone uses the same path

Option B: Git

• Include .bib in your repository
• Push updates after adding references

Option C: Thetapad shared project

• Upload the .bib file
• Collaborate in real-time

Troubleshooting

Reference Not Appearing

Symptom: [?] appears instead of citation

Fixes:

1. Check citation key matches exactly (case-sensitive)
2. Verify .bib file is in the right location
3. Run biber/bibtex and recompile

Export Not Updating

Symptom: New references don't appear in .bib

Fixes:

1. Check "Sync library to BibTeX" is enabled
2. Force sync: Tools → Options → BibTeX → "Sync Now"
3. Verify export path is correct

Duplicate Citation Keys

Symptom: Two papers have the same key

Fixes:

1. Mendeley usually adds a, b, c suffixes
2. Manually edit one entry's citation key
3. Use a more specific key format (include title words)

Encoding Issues

Symptom: Accented characters appear wrong

Fixes:

1. Ensure document uses \usepackage[utf8]{inputenc}
2. Or use LuaLaTeX/XeLaTeX (native Unicode)
3. Check Mendeley's export encoding settings

Mendeley vs Zotero

| Feature | Mendeley | Zotero | |---------|----------|--------| | Price | Free (with limits) | Free | | Storage | 2GB free | 300MB free | | BibTeX export | Built-in | Via extension | | Auto-sync .bib | Yes | Yes (with Better BibTeX) | | PDF annotation | Yes | Yes | | Group libraries | Yes | Yes | | Open source | No | Yes | | LaTeX quality | Good | Excellent (with BBT) |

Both work well. Mendeley is simpler; Zotero (with Better BibTeX) offers more control.

Best Practices

1. One Project, One Export

Export separate .bib files for different projects:

thesis/references.bib
paper-2024/references.bib

Keeps files focused and avoids huge libraries.

2. Verify Before Submission

Before submitting a paper:

• Check all citations resolve
• Verify formatting matches journal style
• Remove unused references

3. Backup Your Library

Mendeley stores data online, but also:

• Export your entire library periodically
• Keep a backup of .bib files
• Don't rely solely on cloud sync

4. Keep Metadata Clean

Good metadata in Mendeley = good BibTeX output:

• Fill in all fields (authors, year, journal)
• Use consistent formatting
• Correct errors when you spot them

Conclusion

Mendeley + Thetapad provides a smooth citation workflow:

1. Collect references with Mendeley browser extension
2. Organize in Mendeley's library
3. Auto-export to BibTeX
4. Cite effortlessly in Thetapad
5. Compile with perfect bibliography

Set it up once, and citations become effortless for every paper you write.

For Zotero users, see our companion guide on Zotero + Thetapad integration.