clinicaltrialsgov-mcp-server

<div align="center"> <h1>clinicaltrialsgov-mcp-server</h1> <p><b>Search ClinicalTrials.gov trials, retrieve study details and results, and match patients to eligible trials via MCP. STDIO or Streamable HTTP.</b> <div>7 Tools • 1 Resource • 1 Prompt</div> </p> </div>

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Public Hosted Server: https://clinicaltrials.caseyjhand.com/mcp

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Overview

Seven tools for searching, discovering, analyzing, and matching clinical trials:

| Tool Name | Description | | :------------------------------------- | :----------------------------------------------------------------------------------------------- | | clinicaltrials_search_studies | Search studies with full-text queries, filters, pagination, sorting, and field selection. | | clinicaltrials_get_study_record | Fetch a single study by NCT ID. Returns the full record: protocol, eligibility, outcomes, arms, interventions, contacts, and locations. | | clinicaltrials_get_study_count | Get total study count for a query without fetching data. Fast statistics and breakdowns. | | clinicaltrials_get_field_values | Discover valid values for API fields (status, phase, study type, etc.) with per-value counts. | | clinicaltrials_get_field_definitions | Browse the study data model field tree — piece names, types, nesting. Supports subtree navigation and keyword search. | | clinicaltrials_get_study_results | Extract outcomes, adverse events, participant flow, and baseline from completed studies. Optional summary mode reduces ~200KB payloads to ~5KB. | | clinicaltrials_find_eligible | Match patient demographics and conditions to eligible recruiting trials. Provide age, sex, conditions, and location to find studies with matching eligibility criteria, contacts, and recruiting locations. |

| Resource | Description | | :------------------------- | :-------------------------------------------------- | | clinicaltrials://{nctId} | Fetch a single clinical trial study by NCT ID. Full JSON. |

| Prompt | Description | | :------------------------ | :--------------------------------------------------------------------------------- | | analyze_trial_landscape | Adaptable workflow for data-driven trial landscape analysis using count + search tools. |

Tools

clinicaltrials_search_studies

Primary search tool with full ClinicalTrials.gov query capabilities.

• Full-text and field-specific queries (condition, intervention, sponsor, location, title, outcome)
• Status and phase filters with typed enum values
• Geographic proximity filtering by coordinates and distance
• Advanced AREA[] Essie expression support for complex queries
• Compact index results by default; pass fields for a full-fidelity projection of specific leaves (a full single record is ~70KB — fetch one with get_study_record)
• Pagination with cursor tokens, sorting by any field

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clinicaltrials_get_study_results

Fetch posted results data for completed studies.

• Outcome measures with statistics, adverse events, participant flow, baseline characteristics
• Section-level filtering (request only the data you need)
• Optional summary mode condenses full results (~200KB) to essential metadata (~5KB per study)
• Batch multiple NCT IDs per call with partial-success reporting
• Separate tracking of studies without results and fetch errors

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clinicaltrials_find_eligible

Match a patient profile to eligible recruiting trials.

• Takes age, sex, conditions, and location as patient demographics
• Builds optimized API queries with demographic filters (age range, sex, healthy volunteers)
• Re-ranks results so studies whose own condition matches a requested condition surface above tangential matches from the upstream fuzzy condition search
• Returns studies with eligibility and location fields for the caller to evaluate
• Provides actionable hints when no studies match (broaden conditions, adjust filters)

Features

Built on @cyanheads/mcp-ts-core:

• Declarative tool/resource/prompt definitions with Zod schemas and format functions
• Unified error handling — handlers throw, framework catches and classifies
• Dual transport: stdio and Streamable HTTP from the same codebase
• Pluggable auth (none, jwt, oauth) for HTTP transport
• Structured logging with optional OpenTelemetry tracing

ClinicalTrials.gov-specific:

• Type-safe client for the ClinicalTrials.gov REST API v2
• Public API — no authentication or API keys required
• Retry with exponential backoff (3 attempts) and rate limiting (~1 req/sec)
• HTML error detection and structured error factories

Getting Started

Public Hosted Instance

A public instance is available at https://clinicaltrials.caseyjhand.com/mcp — no installation required. Point any MCP client at it via Streamable HTTP:

{
  "mcpServers": {
    "clinicaltrialsgov-mcp-server": {
      "type": "streamable-http",
      "url": "https://clinicaltrials.caseyjhand.com/mcp"
    }
  }
}

Self-Hosted / Local

Add to your MCP client config (e.g., claude_desktop_config.json):

{
  "mcpServers": {
    "clinicaltrialsgov-mcp-server": {
      "type": "stdio",
      "command": "bunx",
      "args": ["clinicaltrialsgov-mcp-server@latest"],
      "env": {
        "MCP_TRANSPORT_TYPE": "stdio"
      }
    }
  }
}

Or for Streamable HTTP:

MCP_TRANSPORT_TYPE=http
MCP_HTTP_PORT=3010

Prerequisites

• Bun v1.3.0 or higher (or Node.js >= 24.0.0)

Installation

1. Clone the repository:

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

1. Navigate into the directory:

   cd clinicaltrialsgov-mcp-server

1. Install dependencies:

   bun install

Configuration

All configuration is optional — the server works with defaults and no API keys.

| Variable | Description | Default | | :--------------------------- | :------------------------------------------ | :---------------------------------- | | CT_API_BASE_URL | ClinicalTrials.gov API base URL. | https://clinicaltrials.gov/api/v2 | | CT_REQUEST_TIMEOUT_MS | Per-request timeout in milliseconds. | 30000 | | CT_MAX_PAGE_SIZE | Maximum page size cap. | 200 | | MCP_TRANSPORT_TYPE | Transport: stdio or http. | stdio | | MCP_HTTP_PORT | Port for HTTP server. | 3010 | | MCP_AUTH_MODE | Auth mode: none, jwt, or oauth. | none | | MCP_LOG_LEVEL | Log level (RFC 5424). | info | | LOGS_DIR | Directory for log files (Node.js only). | <project-root>/logs | | OTEL_ENABLED | Enable OpenTelemetry tracing. | false |

Running the Server

Local Development

• Build and run the production version:

  bun run build
  bun run start:http   # or start:stdio

• Run checks and tests:

  bun run devcheck     # Lints, formats, type-checks
  bun run test         # Runs test suite

Docker

docker build -t clinicaltrialsgov-mcp-server .
docker run -p 3010:3010 clinicaltrialsgov-mcp-server

Project Structure

| Directory | Purpose | | :------------------------------ | :---------------------------------------------------- | | src/mcp-server/tools/ | Tool definitions (.tool.ts). | | src/mcp-server/resources/ | Resource definitions (.resource.ts). | | src/mcp-server/prompts/ | Prompt definitions (*.prompt.ts). | | src/services/clinical-trials/ | ClinicalTrials.gov API client and types. | | src/config/ | Environment variable parsing and validation with Zod. | | tests/ | Unit and integration tests. |

Development Guide

See CLAUDE.md for development guidelines and architectural rules. The short version:

• Handlers throw, framework catches — no try/catch in tool logic
• Use ctx.log for request-scoped logging, no console calls
• Register new tools and resources in the index.ts barrel files

Contributing

Issues and pull requests are welcome. Run checks before submitting:

bun run devcheck
bun run test

License

Apache-2.0 — see LICENSE for details.