How to Use the ClinicalTrials.gov MCP in Mastra AI

Build resilient Mastra AI workflows with the ClinicalTrials.gov MCP Server to handle complex medical registry lookups automatically.

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Connect ClinicalTrials.gov MCP to Mastra AI

Create your Vinkius account to connect ClinicalTrials.gov to Mastra AI and route execution through our secure gateway. The platform manages server hosting, runtime updates, and security layers. Configuration requires no manual server provisioning.

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Setup ClinicalTrials.gov with Mastra AI

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Perplexity

Build automated registry workflows

Medical databases frequently timeout or return partial records. Mastra AI wraps the `search_clinical_trials` MCP tool with exponential backoff so your pipeline survives temporary registry outages. If a keyword search fails, your workflow can branch to try alternative condition names. The system keeps working until it finds the right studies.

Filter enrollments via MCP Server

Patient matching requires accurate, up-to-the-minute status checks. Deploy `find_recruiting_trials` inside a recurring Mastra sync to catch newly opened sites immediately. Approvals can be inserted before notifying a patient. A human doctor reviews the flagged studies while the workflow pauses, resuming only when authorized.

Parse complex NCT records reliably

Pulling a 50-page protocol document usually breaks standard API scripts. Calling `get_trial_details` through our managed infrastructure guarantees the full schema arrives cleanly. You feed that raw output into downstream Mastra nodes for summarization or database insertion. The heavy lifting happens off your main application thread.

Setup guide

Set up ClinicalTrials.gov MCP in Mastra AI

Prerequisites

Node.js 18+ and a TypeScript project
@mastra/mcp + @mastra/core packages
Active Vinkius subscription with a valid endpoint token

1

Install dependencies
Run npm install @mastra/mcp @mastra/core plus your preferred model provider (e.g. @ai-sdk/openai).
2

Configure the MCPClient
Create an MCPClient with your Vinkius endpoint as a URL object. Replace [YOUR_TOKEN_HERE] with your token from cloud.vinkius.com.
3

Discover and inject tools
Call mcpClient.listTools() and spread the result into your agent's tools object. All ClinicalTrials.gov tools become native Mastra tools.
4

Run with any model
Swap openai("gpt-4o") for any AI SDK-compatible provider. Call agent.generate() and the agent routes tool calls through MCP automatically.

agent.ts

import { MCPClient } from "@mastra/mcp";
import { Agent } from "@mastra/core/agent";
import { openai } from "@ai-sdk/openai";

const mcpClient = new MCPClient({
  id: "clinicaltrialsgov-mcp-client",
  servers: {
    "clinicaltrialsgov-mcp": {
      url: new URL(
        "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
      ),
    },
  },
});

const agent = new Agent({
  name: "ClinicalTrials.gov Agent",
  model: openai("gpt-4o"),
  instructions: "You have access to ClinicalTrials.gov tools.",
  tools: {
    ...(await mcpClient.listTools()),
  },
});

const result = await agent.generate(
  "List recent ClinicalTrials.gov transactions"
);
console.log(result.text);

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Independent Platform Disclaimer: Vinkius is an independent platform and is not affiliated with, endorsed by, sponsored by, verified by, or otherwise authorized by ClinicalTrials.gov. All third-party trademarks, logos, and brand names are the property of their respective owners. Their use on this website is strictly for informational purposes to identify service compatibility and interoperability.

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Common questions about ClinicalTrials.gov MCP in Mastra AI

Initialize a new MCPClient with your Vinkius URL and spread the returned tools into your Agent configuration. The framework auto-detects the streamable HTTP transport.

Built-in workflow engines handle failures natively. If the registry drops a connection, your agent automatically backs off and tries the query again.

Enable the requireToolApproval flag on your agent configuration. Execution halts when a trial is found, waiting for a doctor to review the NCT record before proceeding.

You can set up scheduled syncs to check specific identifiers repeatedly. The workflow compares the new output against your database and triggers alerts on changes.

Every tool execution runs in a zero-trust, isolated environment. Search terms and NCT identifiers exist only for the duration of the request, ensuring strict compliance with health data standards.

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