Clinical

You can deploy a Clinical MCP Server to securely access clinical data sources (such as patient records or medical guidelines) from an MCP client. This server provides standardized data access through the MCP protocol, enabling safe integration with Microsoft Copilot Studio while supporting enterprise security and HIPAA-compliant workflows.

How to use

Use an MCP client to connect to the Clinical MCP Server URLs and request clinical data or guidelines. The server exposes a dedicated endpoint path that your client can query to retrieve patient data, medical guidelines, and other clinical information. Ensure you access the server over a trusted network and follow your organization’s privacy and security policies.

How to install

Prerequisites include a development environment with Node.js, npm, and Git, plus tools for container or cloud deployment if you plan to run in Azure.

Commands to set up locally from a clone of the Clinical MCP repository are shown below. Run each line exactly as written.

bash
# Clone the Clinical MCP repository
git clone https://github.com/shekhar-ai99/clinical-mcp.git

# Change into the project directory
cd clinical-mcp

# Install dependencies
npm install

# Build and start the server
npm run build && npm run start

# Optional: open port 3000 to access the MCP server locally
# In your environment, forward port 3000 if needed and access /mcp path

Additional sections

Server endpoints. The Local Development URL exposes the MCP interface at a path that ends with /mcp once the server is running and the port is properly forwarded. You will receive an accessible http URL similar to https://your-forwarded-host:port/mcp when you forward the port.

Azure deployment. You can deploy the Clinical MCP Server to Azure using the Azure Developer CLI. After logging in and provisioning, the server will provide an external URL, typically ending with /mcp. Remember to shut down resources when you are done to avoid ongoing costs.

Security and usage notes. Treat clinical data with care, follow HIPAA and local regulations, and configure access controls, network isolation, and auditing for any production deployment. Use secure connections and manage credentials through your organization’s secrets management practices.

Configuration and cleanup notes

Configuration involves pointing your MCP client at one or more server URLs and ensuring the client is allowed to communicate with those endpoints. For cleanup, stop any locally running server and remove any Azure resources if you deployed there.

Troubleshooting tips

If you encounter access issues, verify that port forwarding is active and that the /mcp path is reachable from your client. Check network permissions, firewall rules, and that the server process is running.

Available tools

clinical_connector_import

Import a custom connector from GitHub into Copilot Studio to connect to the Clinical MCP server.

clinical_agent_setup

Create and configure a Copilot Studio agent that uses the Clinical MCP for medical data retrieval.

clinical_mcp_test

Test agent integration against the Clinical MCP to retrieve patient data and guidelines.