📚 Literature MCP

A specialized Model Context Protocol (MCP) server for biological and clinical evidence retrieval. This server provides a structured, agent-friendly interface to the Europe PMC database, enabling LLMs to gather, rank, and synthesize published research.

Built for the Agent4Target ecosystem, it focuses on high-confidence evidence collection for therapeutic targets and disease associations.

🏗️ Architecture & Workflow

The server performs semantic and keyword-based retrieval, transforming raw XML/JSON responses from Europe PMC into clean, machine-readable evidence models.

graph LR
    User([User / LLM Client]) <-->|MCP Protocol| Server[Literature MCP Server]
    
    subgraph "Internal Processing"
        Server --> Router{Tool Router}
        Router --> T1[collect_target_evidence]
        Router --> T2[search_articles]
        Router --> T3[get_article_by_pmid]
        
        T1 & T2 & T3 --> Client[EuropePMCClient]
        Client --> EPMC_API[[Europe PMC REST API]]
    end
    
    subgraph "Ranking Logic"
        Client --> Ranker[Citation & Recency Weighted Ranking]
        Ranker --> Pydantic[Pydantic Result Models]
        Pydantic --> Server
    end

🚀 Quick Start

1. Installation

pip install literature-mcp

2. Running the Server

The server is highly flexible and supports both stdio (standard for Claude Desktop) and HTTP SSE transport.

# Run over stdio (Standard)
literature-mcp --transport stdio

# Run as local HTTP server (SSE)
literature-mcp --port 8002

🛠️ Tools Documentation

`collect_literature_target_evidence`

The primary tool for the Agent4Target workflow. It performs a multi-strategy search for a gene and disease context, returning the most cited and relevant evidence records.

Inputs:
- gene_symbol (required, e.g., "BRAF")
- disease_id (optional, e.g., "EFO_0000311")
- limit (max records, default: 15)

`search_literature_articles`

A flexible search tool that accepts raw Europe PMC query strings (e.g., AUTHOR:"Vogelstein B" AND GENE:"KRAS").

Inputs: query (string)

`get_literature_article_by_pmid`

Retrieves full structured metadata for a specific article.

Inputs: pmid (string)

`get_literature_service_metadata`

Returns information about the underlying Europe PMC client, API rate limits, and health status.

⚙️ Configuration

Variable	Default	Description
`LITERATURE_MCP_EUROPE_PMC_SEARCH_URL`	`https://www.ebi.ac.uk/...`	REST API endpoint.
`LITERATURE_MCP_HTTP_PORT`	`8002`	Port for SSE transport.
`LITERATURE_MCP_REQUEST_TIMEOUT_S`	`30`	Network timeout for API calls.
`LITERATURE_MCP_LOG_LEVEL`	`INFO`	Verbosity of server logs.

🖥️ Usage in Claude Desktop

Add this to your claude_desktop_config.json:

{
  "mcpServers": {
    "literature-mcp": {
      "command": "literature-mcp",
      "args": ["--transport", "stdio"],
      "env": {
        "LITERATURE_MCP_LOG_LEVEL": "DEBUG"
      }
    }
  }
}

🧪 Development

The project uses uv for modern, fast dependency management.

# Clone and setup
git clone https://github.com/your-org/literature-mcp
cd literature-mcp
uv sync

# Run tests
uv run pytest

Literature MCP