MedCP: Medical Model Context Protocol

Overview

MedCP transforms Claude Desktop into a powerful medical AI assistant by providing secure, local access to electronic health records and biomedical knowledge graphs. Process sensitive health data entirely on your machine while delivering instant access to clinical insights.

Key Features

• Local Processing - All data processing happens on your machine
• EHR Integration - Query electronic health records with natural language
• Biomedical Knowledge - Access comprehensive drug-disease associations and protein interactions
• Real-time Analysis - Instant clinical decision support
• Secure Storage - Credentials encrypted in OS keychain

Prerequisites

System Requirements

• Claude Desktop 1.0.0+ with DXT support
• Operating System: macOS 11+ or Windows 10+
• Python 3.11+ with uv package manager
• Memory: 8GB RAM minimum, 16GB recommended

Install Required Software

1. Download Claude Desktop Visit claude.ai/download and install the latest version.

2. Install UV Package Manager

macOS:

First install homebrew if not installed already.

Then, deactivate any conda or virtual environment and check the native python version on your mac:

python3 --version

If your python version is older than 3.13, try to get the most up-to-date python installed:

brew install python

Then install the uv package manager via homebrew:

brew install uv

Windows:

Install uv via powershell:

powershell -c "irm https://astral.sh/uv/install.ps1 | iex"

Linux:

Install uv via bash script:

curl -LsSf https://astral.sh/uv/install.sh | sh

Installation

Quick Install

1. Download the Extension

   • Go to Releases
   • Download the latest MedCP.dxt file

2. Install in Claude Desktop

   • Double-click the MedCP.dxt file
   • Claude Desktop will open the installation dialog
   • Click "Install"

3. Configure Databases

   • Complete the configuration wizard that appears
   • Enter your database credentials (details below)

That's it!

Configuration

After installation, you'll need to configure your database connections in Claude Desktop:

Settings → Extensions → MedCP

Biomedical Knowledge Graph

MedCP uses the SPOKE knowledge graph by default (Morris et al., 2023), which contains comprehensive biomedical relationships including drug-disease associations, protein interactions, and biological pathways.

Parameter	Description	Example
Knowledge Graph URI	Neo4j connection URI	bolt://your-neo4j-server:7687
Username	Neo4j database username	your_username
Password	Neo4j database password	your_secure_password
Database Name	Neo4j database name	spoke (default)

Electronic Health Records

Configure access to your clinical database. For UCSF users, see the UCSF Research Data portal for access information.

Parameter	Description	Example
Clinical Records Server	SQL Server hostname	your-ehr-server.hospital.org
Database Name	Clinical database name	OMOP_DEID
Username	Database username	clinical_user
Password	Database password	secure_clinical_password

Optional Settings

Parameter	Description	Default
MedCP Namespace	Tool prefix for organization	MedCP
Log Level	Logging verbosity	INFO

Security Note: All sensitive credentials are automatically encrypted and stored in your operating system's secure keychain.

Usage Examples

Query Patient Records

"Find all patients diagnosed with diabetes in the last 6 months and summarize their HbA1c trends"

Drug Interaction Analysis

"Check for interactions between metformin, lisinopril, and atorvastatin for a 65-year-old patient with CKD stage 3"

Clinical Guidelines

"What are the current evidence-based guidelines for treating community-acquired pneumonia in elderly patients?"

Biomedical Research

"Find protein targets associated with Alzheimer's disease and identify potential drug compounds that interact with these proteins"

Troubleshooting

Extension Not Loading

1. Verify Claude Desktop supports DXT extensions
2. Check that all required configuration fields are completed
3. Restart Claude Desktop after configuration changes

Database Connection Issues

1. Verify server URLs are accessible from your network
2. Check that credentials are valid and not expired
3. Ensure firewall allows database connections
4. Test connectivity outside Claude Desktop if possible

Performance Issues

1. Limit query result sizes for large datasets
2. Use specific date ranges in clinical queries
3. Check available system memory

Need Help?

• Documentation: Check the configuration examples above
• Bug Reports: Create an issue
• Security Issues: Contact the development team privately

License

MedCP is released under the MIT License.

Authors and Maintainers

MedCP is developed and maintained by the Baranzini Lab at UCSF.

• Wanjun Gu - [email protected]
• Gianmarco Bellucci - [email protected]

Acknowledgments

• SPOKE Knowledge Graph: Morris et al., 2023
• UCSF Clinical Data: UCSF Research Data Portal
• Desktop Extensions: Built on Anthropic's DXT specification
• Model Context Protocol: Enables secure local AI integration

Download MedCP Extension | Report Issues | Contact