Clinicaltrialsgov MCP Server

🚀 ClinicalTrials.gov MCP Server

Empower your AI agents with direct access to the official ClinicalTrials.gov database! This MCP (Model Context Protocol) server offers a robust, developer - friendly interface to the official ClinicalTrials.gov v2 API, enabling LLMs and AI agents to search, retrieve, and analyze clinical study data programmatically. Built on the [cyanheads/mcp - ts - template](https://github.com/cyanheads/mcp - ts - template), it follows a modular architecture with robust error handling, logging, and security features.

🚀 Quick Start

The ClinicalTrials.gov MCP Server serves as a bridge, allowing MCP - compatible applications (such as advanced AI assistants, IDE extensions, or custom research tools) to interact directly and efficiently with the official ClinicalTrials.gov database. Instead of complex API integration or manual searches, your tools can use this server to automate clinical research workflows, gain research insights, integrate clinical trial data into AI - driven research, and support regulatory and compliance workflows.

✨ Features

Core Utilities

• Logging: Structured, configurable logging (file rotation, stdout JSON, MCP notifications) with sensitive data redaction.
• Error Handling: Centralized error processing, standardized error types (McpError), and automatic logging.
• Configuration: Environment variable loading (dotenv) with comprehensive validation using Zod.
• Input Validation/Sanitization: Uses zod for schema validation and custom sanitization logic.
• Request Context: Tracking and correlation of operations via unique request IDs using AsyncLocalStorage.
• Type Safety: Strong typing enforced by TypeScript and Zod schemas.
• HTTP Transport: High - performance HTTP server using Hono, featuring session management and authentication support.
• Authentication: Robust authentication layer supporting JWT and OAuth 2.1, with fine - grained scope enforcement.
• Deployment: Multi - stage Dockerfile for creating small, secure production images with native dependency support.

ClinicalTrials.gov Integration

• Official API Integration: Comprehensive access to ClinicalTrials.gov v2 API endpoints with automatic JSON parsing.
• Advanced Search Capabilities: Complex query construction with filters for study status, geographic location, conditions, interventions, and sponsors.
• Full Study Metadata: Retrieve complete trial data including protocols, eligibility criteria, study design, outcomes, sponsors, and contact information.
• Flexible Field Selection: Choose specific data fields to retrieve for efficient API usage and reduced response sizes.
• Pagination Support: Handle large result sets with built - in pagination using pageSize and pageToken parameters.
• Data Cleaning: Automatically cleans and simplifies redundant information from API responses for easier consumption.
• Rate Limiting Compliance: Built - in request throttling to comply with ClinicalTrials.gov API guidelines.

📦 Installation

Prerequisites

• Node.js (>=18.0.0)
• npm (comes with Node.js)

MCP Client Settings

Add the following to your MCP client's configuration file (e.g., cline_mcp_settings.json). This configuration uses npx to run the server, which will automatically install the package if not already present:

{
  "mcpServers": {
    "clinicaltrialsgov-mcp-server": {
      "command": "npx",
      "args": ["clinicaltrialsgov-mcp-server"],
      "env": {
        "MCP_LOG_LEVEL": "info"
      }
    }
  }
}

If running manually (not via MCP client for development or testing)

Install via npm

npm install clinicaltrialsgov-mcp-server

Alternatively Install from Source

1. Clone the repository:

git clone https://github.com/cyanheads/clinicaltrialsgov-mcp-server.git
cd clinicaltrialsgov-mcp-server

2. Install dependencies:

npm install

3. Build the project:

npm run build

📚 Documentation

Configuration

Environment Variables

Configure the server using environment variables. For local development, these can be set in a .env file at the project root or directly in your environment. Otherwise, you can set them in your MCP client configuration as shown above.

Project Structure

The codebase follows a modular structure within the src/ directory:

src/
├── index.ts              # Entry point: Initializes and starts the server
├── config/               # Configuration loading (env vars, package info)
│   └── index.ts
├── mcp-server/           # Core MCP server logic and capability registration
│   ├── server.ts         # Server setup, capability registration
│   ├── transports/       # Transport handling (stdio, http)
│   └── tools/            # MCP Tool implementations (subdirs per tool)
├── services/             # External service integrations
│   └── clinical-trials-gov/ # ClinicalTrials.gov API client and types
├── types-global/         # Shared TypeScript type definitions
└── utils/                # Common utility functions (logger, error handler, etc.)

For a detailed file tree, run npm run tree or see docs/tree.md.

Tools

The ClinicalTrials.gov MCP Server provides a comprehensive suite of tools for clinical trial research, callable via the Model Context Protocol.

Note: All tools support comprehensive error handling and return structured JSON responses.

💻 Usage Examples

Basic Usage

Comprehensive usage examples are available in the examples/ directory:

• List Studies
• Get Study Details

🔧 Technical Details

Core Capabilities: ClinicalTrials.gov Tools

This server equips your AI with specialized tools to interact with the ClinicalTrials.gov database:

📄 License

This project is licensed under the Apache License 2.0 - see the LICENSE file for details.