<p align="center"> <img src="logo.jpg" alt="BioCite-MCP Logo" width="300"> </p>

BioCite-MCP 🧬

BioCite-MCP is an advanced Model Context Protocol (MCP) server that acts as a real-time bridge between LLMs and academic literature databases (Europe PMC & Crossref). It eliminates citation hallucinations by forcing AI models to retrieve verified, peer-reviewed paper metadata and real DOIs directly within their workflow.

🌟 Key Features

🔍 Literature Discovery

• `search_literature`: Query Europe PMC for real biological papers. Returns structured metadata including DOIs and abstracts.
• `find_related_papers`: Discovers semantically related research using Europe PMC's Recommendations engine with an automated Citations/References fallback.

📝 Citation & Formatting

• `resolve_citation`: Converts any DOI into publication-ready citation strings (APA or Nature style).
• `export_bibtex`: Retrieves professional BibTeX entries directly via Crossref content negotiation.

🛡️ Manuscript Auditing & Support

• `audit_manuscript`: Scans your text for DOIs to verify them and flags potential citations that lack DOIs.
• `summarize_paper`: Fetches abstracts and prepares high-quality summarization prompts optimized for LLMs like Claude.
• `check_duplicate_citations`: Uses fuzzy matching (rapidfuzz) to identify and group duplicate research in your lists.

📚 Integration

• `push_to_zotero`: Seamlessly add verified papers to your Zotero library via the Web API.

🚀 Installation

pip install biocite-mcp

Note: For development, use `pip install -e .` in the repository root.

🔧 Configuration

Add biocite-mcp to your MCP host configuration (e.g., claude_desktop_config.json):

{
  "mcpServers": {
    "biocite-mcp": {
      "command": "python",
      "args": ["-m", "biocite_mcp"]
    }
  }
}

🛠️ Usage Examples

1. Search: "Find recent papers about DREB2A drought stress in tomato."
2. Resolve: "Format the citation for DOI 10.1093/jxb/erx393 in Nature style."
3. Analyze: "Audit this manuscript draft for citation accuracy: [Your Text Here]" (Pro-tip: Use Claude's Filesystem MCP to read your manuscript file and pipe the content directly into this tool!)
4. Export: "Give me the BibTeX for 10.1111/j.1365-313X.2006.02701.x"

📜 License

This project is licensed under the MIT License - see the LICENSE file for details.

Developed by ZaEyAsa — Your Advanced Agentic Bio-Citation Assistant.