Clinicaltrialsgov Mcp Server

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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; outcomeLimit / adverseEventLimit cap full mode without leaving it.
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. Protocol JSON with capped locations/outcomes/references and results replaced by counts; omissions reported with the tool that retrieves them.

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
• Bounds each candidate to the sites matching the requested location (capped by locationLimit) rather than every site the study registers worldwide, adds the nearest recruiting site when none of the matched ones is open, and discloses what was omitted
• 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
   

2. Navigate into the directory:

   cd clinicaltrialsgov-mcp-server
   

3. 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.