-
securityA
license-
qualityProvides access to the ClinicalTrials.gov AACT database, enabling analysis of clinical trial data, tracking development trends, and generating therapeutic landscape insights.
Last updated -
16
GPL 3.0
The ClinicalTrials.gov MCP Server enables AI agents to programmatically access and analyze the ClinicalTrials.gov database through three core tools:
Search Studies (clinicaltrials_search_studies) - Find clinical trials using query terms (conditions, interventions, locations, sponsors) and filters, with support for pagination, sorting, geographic filtering, and advanced Essie expression syntax.
Retrieve Study Details (clinicaltrials_get_study) - Fetch comprehensive or summary information for specific studies by NCT ID, including protocols, eligibility criteria, outcomes, sponsors, and locations, with flexible field selection and markup format options.
Analyze Trends (clinicaltrials_analyze_trends) - Perform statistical analysis on up to 5000 studies, aggregating data by status, country, sponsor type, or phase to identify research patterns and trends.
Key Applications:
Automate clinical research workflows and integrate trial data into AI-driven applications
Support regulatory submissions, compliance workflows, and competitive intelligence
Enable evidence-based decision making through comprehensive trial analysis
Streamline clinical trial reviews and market research
Technical Features: Built on the official ClinicalTrials.gov v2 API with robust error handling, rate limiting, data cleaning, input validation, and TypeScript type safety for reliable programmatic access.
Provides the project repository on GitHub for access to source code and documentation.
Uses Hono as a high-performance HTTP server featuring session management, CORS, and IP-based rate limiting.
Supports returning clinical trial data in markdown format for improved readability in AI responses.
Requires Node.js (>=18.0.0) as the runtime environment for the MCP server.
Distributes the server via npm package management system, allowing for easy installation.
Uses Prettier for consistent code formatting during development.
Built with TypeScript for type safety and robust error handling when interacting with the ClinicalTrials.gov database.
Implements input validation and sanitization using Zod schema validation for secure API interactions.
clinicaltrialsgov-mcp-server
Empower your AI agents with direct access to the ClinicalTrials.gov database!
Model Context Protocol (MCP) Server providing a robust, developer-friendly interface to the official ClinicalTrials.gov v2 API. Enables LLMs and AI agents to search, retrieve, and analyze clinical study data programmatically.
Built on the cyanheads/mcp-ts-template, this server follows a modular architecture with robust error handling, logging, and security features.
🚀 Core Capabilities: ClinicalTrials.gov Tools 🛠️
This server equips your AI with specialized tools to interact with the ClinicalTrials.gov database:
Tool Name | Description | Example |
Searches for clinical studies using a combination of query terms and filters. Supports pagination, sorting, and geographic filtering. | ||
Fetches one or more clinical studies from ClinicalTrials.gov by their NCT IDs. Returns either complete study data or concise summaries for each. | ||
Performs a statistical analysis on a set of clinical trials, aggregating data by status, country, sponsor, or phase. Use specific query parameters to refine the analysis and filter the studies included in the analysis. The tool can handle up to 5000 studies per analysis. |
Table of Contents
| Overview | Features | Installation | Configuration | Project Structure | Tools | Development & Testing | License
Overview
The ClinicalTrials.gov MCP Server acts as a bridge, allowing applications (MCP Clients) that understand the Model Context Protocol (MCP) – like advanced AI assistants (LLMs), 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 leverage this server to:
Automate clinical research workflows: Search for clinical trials, fetch detailed study metadata, and analyze trial characteristics programmatically.
Gain research insights: Access comprehensive trial data including study protocols, eligibility criteria, outcomes, sponsors, and locations without leaving the host application.
Integrate clinical trial data into AI-driven research: Enable LLMs to conduct clinical trial reviews, analyze research trends, and support evidence-based decision making.
Support regulatory and compliance workflows: Retrieve structured data for regulatory submissions, competitive intelligence, and market research.
Built on the robust mcp-ts-template, this server provides a standardized, secure, and efficient way to expose ClinicalTrials.gov functionality via the MCP standard. It achieves this by integrating with the official ClinicalTrials.gov v2 API, ensuring compliance with rate limits and providing comprehensive error handling.
Developer Note: This repository includes a .clinerules file that serves as a developer cheat sheet for your LLM coding agent with quick reference for the codebase patterns, file locations, and code snippets.
Features
Core Utilities
Leverages the robust utilities provided by the mcp-ts-template:
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
zodfor 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
Dockerfilefor 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
pageSizeandpageTokenparameters.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
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
Clone the repository:
git clone https://github.com/cyanheads/clinicaltrialsgov-mcp-server.git cd clinicaltrialsgov-mcp-serverInstall dependencies:
npm installBuild the project:
npm run build
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.
Variable | Description | Default |
| Transport mechanism:
or
. |
|
| Port for the HTTP server (if
). |
|
| Host address for the HTTP server (if
). |
|
| Comma-separated list of allowed origins for CORS (if
). | (none) |
| Logging level (
,
,
,
,
,
,
,
). |
|
| Authentication mode for HTTP:
or
. |
|
| Required for Minimum 32-character secret key for JWT authentication. | (none) |
| Directory for caching ClinicalTrials.gov API data. |
|
| Directory for log file storage. |
|
| Runtime environment (
,
). |
|
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.
Tool Name | Description | Key Arguments |
| Searches for clinical studies using queries, filters, and pagination. |
,
,
,
,
,
,
|
| Fetches detailed information for one or more studies by NCT ID. |
,
,
,
|
| Performs statistical analysis on a set of studies. |
,
,
|
Note: All tools support comprehensive error handling and return structured JSON responses.
Examples
Comprehensive usage examples for each tool are available in the examples/ directory.
clinicaltrials_search_studies: View Exampleclinicaltrials_get_study: View Exampleclinicaltrials_analyze_trends: View Example
Development & Testing
Development Scripts
# Build the project (compile TS to JS in dist/ and make executable)
npm run build
# Clean build artifacts
npm run clean
# Clean build artifacts and then rebuild the project
npm run rebuild
# Format code with Prettier
npm run format
# Generate a file tree representation for documentation
npm run tree
Testing
This project uses Vitest for unit and integration testing.
# Run all tests once
npm test
# Run tests in watch mode
npm run test:watch
# Run tests and generate a coverage report
npm run test:coverage
Running the Server
# Start the server using stdio (default)
npm start
# Or explicitly:
npm run start:stdio
# Start the server using HTTP transport
npm run start:http
# Test the server locally using the MCP inspector tool (stdio transport)
npm run inspector
# Test the server locally using the MCP inspector tool (http transport)
npm run inspector:http
License
This project is licensed under the Apache License 2.0 - see the LICENSE file for details.
remote-capable server
The server can be hosted and run remotely because it primarily relies on remote services or has no dependency on the local environment.
Empowers AI agents with direct access to the official ClinicalTrials.gov database, enabling programmatic searching, retrieval, and analysis of clinical study data through a Model Context Protocol interface.
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