Mendeley + Thetapad: Seamless Citation Management

Why Mendeley + Thetapad?

Managing citations is one of the most time-consuming parts of academic writing. Manually typing BibTeX entries is tedious and error-prone. Tracking down correct metadata for each source takes hours.

Mendeley solves the collection problem. It stores your papers, extracts metadata, and organizes your research library. Combined with Thetapad's LaTeX editing, you get a complete academic writing workflow where citations flow automatically from your reading to your writing.

What Mendeley Offers

Mendeley is one of the most popular reference managers, used by millions of researchers worldwide. Key features include:

• Paper storage and organization - Keep all your PDFs in one searchable library
• Automatic metadata extraction - Mendeley reads PDF metadata and fetches missing information
• PDF annotation - Highlight, comment, and take notes directly on papers
• Related research discovery - Find papers similar to those in your library
• Collaboration with groups - Share libraries with research teams
• BibTeX export - Generate bibliography files for LaTeX

The Mendeley + Thetapad combination gives you the best of both worlds: professional reference management and professional typesetting.

Setting Up the Integration

Step 1: Install Mendeley Desktop

If you haven't already installed Mendeley:

1. Download from mendeley.com/download-desktop
2. Install the application for your operating system
3. Create a Mendeley account or sign in
4. Import your existing references (from EndNote, Zotero, or BibTeX files)
5. Install the browser extension for easy paper capture

Step 2: Configure BibTeX Export

Mendeley can automatically export your library to a .bib file. This is the key integration point:

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. Point it to your project folder:

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

6. Set Citation Key format (recommended: AuthorYear)
7. Click OK to save settings

The export happens automatically whenever you add or modify references.

Step 3: Configure Citation Key Format

Citation keys are how you reference papers in your LaTeX document. Good keys are memorable and unique:

Available formats in Mendeley:

• AuthorYear → smith2024
• AuthorTitleYear → smithMachineLearning2024
• AuthorYearTitle → smith2024MachineLearning

For most users, AuthorYear works well. If you frequently cite multiple papers by the same author in the same year, consider AuthorTitleYear for disambiguation.

Step 4: Link to Your Thetapad Project

In your LaTeX document, add the bibliography configuration:

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

Upload your references.bib file to your Thetapad project, and citations will resolve automatically.

The Daily Workflow

Once set up, the daily workflow is simple and automatic.

Adding New References

1. Find a paper you want to cite while reading or researching
2. Import to Mendeley using one of these methods:
   • Click the Mendeley browser extension on an article page
   • Drag and drop a PDF into the Mendeley library
   • Import from a database using DOI or identifier
   • Add manually for books or unusual sources
3. Verify metadata - Mendeley usually extracts correct information, but check author names, year, and journal
4. Mendeley exports to your .bib file automatically
5. In Thetapad: Use the citation key immediately

Citing in Your Document

Biblatex provides flexible citation commands:

% Author (Year) style - for narrative citations
\textcite{smith2024}  % Output: Smith (2024)
 
% (Author, Year) style - for parenthetical citations
\parencite{smith2024}  % Output: (Smith, 2024)
 
% Multiple citations
\parencite{smith2024,jones2023}  % Output: (Smith, 2024; Jones, 2023)
 
% With page numbers
\parencite[p. 42]{smith2024}  % Output: (Smith, 2024, p. 42)
 
% Pre-text and post-text
\parencite[see][ch. 3]{smith2024}  % Output: (see Smith, 2024, ch. 3)
 
% Author only
\citeauthor{smith2024}  % Output: Smith
 
% Year only
\citeyear{smith2024}  % Output: 2024
 
% Full citation in text
\fullcite{smith2024}  % Output: Full bibliographic entry

What Your Bibliography File Looks Like

Mendeley exports clean BibTeX entries:

@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},
  abstract = {This paper presents...}
}
 
@book{jones2023,
  author = {Jones, Robert},
  title = {Introduction to Data Science},
  publisher = {Academic Press},
  year = {2023},
  isbn = {978-0123456789}
}

Mendeley maintains this file automatically as you add references.

Optimizing the Workflow

Customizing Citation Keys

If the default key format doesn't suit your needs:

1. Open Mendeley Preferences → BibTeX
2. Set Document ID to your preferred format:
   • AuthorYear → smith2024 (simple, memorable)
   • AuthorTitleYear → smithMachineLearning2024 (more unique)
   • AuthorYearTitle → smith2024MachineLearning (year first for sorting)

You can also manually edit individual citation keys in Mendeley if needed.

Organizing References for Large Projects

For theses and long documents with many references:

By project:

• 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

By chapter:

• Use subfolders for different chapters or sections
• Consider separate .bib files per chapter for very large projects

By source type:

• Organize primary sources, secondary sources, methods references
• Makes it easier to ensure completeness

Handling Special Characters

Mendeley handles most special characters automatically, but watch for:

Accented names:

author = {M{\"u}ller, Hans}  % ü encoded as \"u
author = {García, María}    % Direct UTF-8 if using modern LaTeX

Math in titles:

title = {Analysis of $O(n \log n)$ Algorithms}  % Math symbols need $...$

Unusual punctuation:

title = {{JavaScript}: The {Good Parts}}  % Braces preserve capitalization

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

Citation Styles

Different journals require different citation formats. Biblatex handles this through style options:

% Common styles
\usepackage[style=authoryear]{biblatex}    % Smith (2024)
\usepackage[style=numeric]{biblatex}       % [1]
\usepackage[style=alphabetic]{biblatex}    % [Smi24]
\usepackage[style=apa]{biblatex}           % APA format
\usepackage[style=ieee]{biblatex}          % IEEE format
\usepackage[style=chicago-authordate]{biblatex}  % Chicago

Your .bib file stays the same—only the style changes how citations appear.

Collaboration with Mendeley Groups

Shared Bibliography for Team Projects

Mendeley Groups enable shared reference libraries:

1. Create a Mendeley Group for your project
2. Add team members to the group
3. Everyone adds references to the shared library
4. Export the group library to a shared .bib file
5. All collaborators use the same references

Syncing the Exported File

For team access to the .bib file:

Option A: Shared folder (Dropbox/OneDrive/Google Drive)

• Export Mendeley to a cloud-synced folder
• Everyone configures the same path
• Changes sync automatically

Option B: Git repository

• Include .bib in your project repository
• Push updates after adding references
• Team pulls changes with their normal workflow

Option C: Thetapad shared project

• Upload the .bib file to Thetapad
• Collaborate in real-time on both document and references
• Update the .bib file when references change

Resolving Conflicts

When multiple people add references:

• Mendeley handles duplicates by comparing DOIs and metadata
• Citation key conflicts get automatic suffixes (a, b, c)
• Review the shared library periodically for duplicate cleanup

Troubleshooting

Reference Not Appearing

Symptom: [?] appears instead of citation in the compiled document

Common causes and fixes:

1. Citation key mismatch - Keys are case-sensitive

   \cite{Smith2024}  % Wrong if key is smith2024
   \cite{smith2024}  % Right

2. Missing .bib file - Verify file is uploaded and path is correct

   \addbibresource{references.bib}  % File must exist

3. Need to recompile - Biber/BibTeX requires multiple passes

   • In Thetapad, compile twice
   • Check the bibliography section appears

4. Backend mismatch - Using bibtex command with biber backend

   \usepackage[backend=biber]{biblatex}  % Use biber
   % or
   \usepackage[backend=bibtex]{biblatex}  % Use bibtex

Export Not Updating

Symptom: New references don't appear in .bib file

Fixes:

1. Verify "Sync library to BibTeX" is enabled in preferences
2. Force sync: Tools → Options → BibTeX → "Sync Now"
3. Check export path is correct and writable
4. Restart Mendeley if sync seems stuck
5. Check if the reference is actually in the folder you're exporting

Duplicate Citation Keys

Symptom: Two papers have the same key, causing confusion

Fixes:

1. Mendeley usually adds a, b, c suffixes automatically
2. Manually edit one entry's citation key in Mendeley
3. Use a more specific key format (include title words)
4. Check for actual duplicate entries in your library

Encoding Issues

Symptom: Accented characters display incorrectly

Fixes:

1. Use modern LaTeX with UTF-8 support:

   \usepackage[utf8]{inputenc}  % For pdfLaTeX

2. Or use LuaLaTeX/XeLaTeX which handle Unicode natively

3. Check Mendeley's export encoding in BibTeX preferences

4. Manually fix specific entries with LaTeX escapes:

   author = {M{\"u}ller}  % Instead of Müller

Missing Fields

Symptom: Bibliography entries missing information

Fixes:

1. Check the entry in Mendeley and fill in missing fields
2. Use Mendeley's metadata lookup (right-click → Look Up)
3. Manually add critical fields like DOI, pages, volume
4. For arXiv papers, add the eprint field

Mendeley vs Zotero

Both are excellent reference managers. Here's how they compare:

| Feature | Mendeley | Zotero | |---------|----------|--------| | Price | Free (with storage limits) | Free (more generous limits) | | Cloud storage | 2GB free, paid for more | 300MB free, WebDAV unlimited | | BibTeX export | Built-in, automatic | Via Better BibTeX extension | | Auto-sync .bib | Yes | Yes (with Better BibTeX) | | PDF annotation | Yes, built-in | Yes, built-in | | Group libraries | Yes, with sharing | Yes, with sharing | | Open source | No | Yes | | Citation key control | Limited | Extensive (with BBT) | | Browser integration | Good | Excellent | | LaTeX export quality | Good | Excellent (with BBT) |

Choose Mendeley if: You want simpler setup and built-in BibTeX export

Choose Zotero if: You want more control over citation keys and export format, or prefer open source

Both integrate well with Thetapad through the standard BibTeX format.

Best Practices

1. One Project, One Export

Export separate .bib files for different projects:

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

This keeps files focused, improves compilation speed, and avoids including irrelevant references.

2. Verify Before Submission

Before submitting a paper:

• Compile and check all citations resolve (no [?] markers)
• Verify formatting matches journal style requirements
• Remove unused references with \nocite{*} or package options
• Check author names, years, and journal titles for accuracy
• Verify DOIs and links work

3. Backup Your Library

Mendeley stores data online, but also:

• Export your entire library periodically as backup
• Keep local copies of .bib files
• Don't rely solely on cloud sync for important projects
• Include .bib files in version control

4. Keep Metadata Clean

Good metadata in Mendeley produces good BibTeX output:

• Fill in all relevant fields (authors, year, journal, volume, pages)
• Use consistent formatting for author names
• Correct errors when you spot them
• Add DOIs for reliable linking
• Review imported metadata for accuracy

5. Regular Library Maintenance

Periodically review your library:

• Merge duplicate entries
• Update incomplete metadata
• Remove papers you no longer need
• Organize into logical folders
• Check for broken citations in active projects

Conclusion

Mendeley + Thetapad provides a smooth, professional citation workflow:

1. Collect references with Mendeley browser extension
2. Organize in Mendeley's library with folders and tags
3. Annotate PDFs while reading
4. Auto-export to BibTeX without manual action
5. Cite effortlessly in Thetapad with citation commands
6. Compile with a perfectly formatted bibliography

Set it up once, maintain your library as you research, and citations become effortless for every paper you write.

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