CERCA – Citation Extraction & Reference Checking Assistant

CERCA is an open-source research tool that supports verification of bibliographic references in scientific manuscripts. It extracts references from PDF files and checks their existence and consistency against authoritative metadata sources, producing explainable diagnostics, audit logs, and reproducible reports.

Key Features

• 📄 Flexible Reference Input:
  • Drag-and-Drop: Parse references automatically from PDF files.
  • Manual Entry Paste reference lists directly for quick checks.
• 🔍 Reference verification using Crossref, OpenAlex and Zenodo metadata
• 📊 Match scores based on title, authors, and DOI similarity
• Interactive Dashboard:
  • View real-time Pass/Fail statistics and verification rates.
  • Color-coded status badges for quick visual assessment.
• 📁 Export Data: Save verification reports for further analysis.
  • 🧾CSV export for analysis
  • 🧾 Diagnosis report (TXT)
• 🪵 Audit log for transparency and reproducibility
• 🔎 Right-click search (Google / Google Scholar) for manual inspection
• 🔒 Local privacy by design — PDFs never leave your machine

📦 How to Run

Windows

1. Download Cerca_windows.zip.
2. Unzip the file.
3. Double-click Cerca-1.0-alpha.jar.

If Windows shows a security warning, choose More info → Run anyway.

macOS

1. Download Cerca_mac.zip.
2. Unzip it.
3. Right-click Cerca-1.0-alpha.jar and select Open.
4. Note: Since this is an unverified alpha app, you may need to go to System Settings > Privacy & Security to allow it to run.

Linux

1. Download Cerca_linux.zip.
2. Unzip it.
3. Open a terminal in that folder and run:
   ```bash
   java -jar Cerca-1.0-alpha.jar

🛠 Requirements

CERCA is a Java desktop application built with JavaFX.

To run CERCA, you need:

• Java 17 or newer
• A Java Runtime Environment that includes JavaFX
• I recommend installing Azul Zulu JRE with JavaFX

🔒Privacy & Local Processing

CERCA is designed with researcher privacy in mind.

• All PDF parsing and reference extraction are performed locally
• Manuscripts are never uploaded, stored, or shared
• CERCA performs metadata-only lookups (e.g., DOI, title, authors)

How It Works

1. A PDF file is parsed locally to extract bibliographic references
2. Each reference is queried against:
3. Crossref
4. Zenodo
5. OpenAlex
6. Metadata fields (title, authors, DOI) are compared
7. CERCA assigns:
8. A match score
9. A status (PASS / CHECK / FAIL)
10. A short diagnostic explanation
11. Results can be saved as:
12. TXT report (diagnosis)
13. CSV table
14. Audit logs
    • Logs are saved for transparency and reproducibility

Status Definitions

• PASS – Strong metadata agreement with authoritative sources
• CHECK – Partial or ambiguous match; manual inspection recommended
• FAIL – No reliable metadata match found at time of verification

CERCA is an experimental tool. It does not replace manual verification.

Outputs

CERCA generates the following artifacts:

• TXT report – Summary and per-reference diagnostics
• CSV file – Structured results for analysis or editorial review
• Audit log – Timestamped record of verification steps

These outputs support reproducibility, transparency, and review documentation.

Intended Use

CERCA is intended for:

• Researchers performing final manuscript checks
• Reviewers assessing reference consistency
• Editors supporting editorial quality control
• Meta-research and reproducibility workflows

Limitations

• Verification depends on availability and correctness of external metadata
• Some valid references (e.g., books, technical reports, older works) may not be indexed
• Match scores are heuristic and intended to support human analysis

License

This project is licensed under the
GNU Affero General Public License, Version 3.0 (AGPL-3.0).

See the LICENSE file for details.

Third-Party Credits

This software uses the CERMINE library, licensed under GNU AGPL v3.

CERMINE
Copyright © Centre for Open Science

Dominika Tkaczyk, Paweł Szostek, Mateusz Fedoryszak,
Piotr Jan Dendek, Łukasz Bolikowski

CERMINE: automatic extraction of structured metadata from scientific literature.
International Journal on Document Analysis and Recognition, 2015,
Vol. 18, No. 4, pp. 317–335, DOI: 10.1007/s10032-015-0249-8

Citation

If you use CERCA in your research, please cite it as research software.

Author

Lidiany Cerqueira, PhD
Computer Science Researcher

Acknowledgments

CERCA was developed to support rigorous, transparent, and responsible research practices.