MSBaseAgent

An MCP (Model Context Protocol) server for querying the UCSF Multiple Sclerosis medical database for rapid clinical data retrieval.

Features

• Query MS Database: Execute SQL queries on the UCSF Multiple Sclerosis medical database
• List Available Tables: Discover all available clinical data tables with schema information
• Pre-configured Access: All database connection parameters are pre-configured - no setup required!
• Read-Only Security: Only SELECT, SHOW, DESCRIBE, and EXPLAIN queries allowed

Installation

From GitHub (using uvx)

uvx --from git+https://github.com/BaranziniLab/MSBaseAgent msbaseagent

Local Installation

cd MSBaseAgent
pip install -e .

Usage

As an MCP Server

Add to your MCP client configuration (e.g., Claude Desktop):

{
  "mcpServers": {
    "msbaseagent": {
      "command": "uvx",
      "args": ["--from", "git+https://github.com/BaranziniLab/MSBaseAgent", "msbaseagent"]
    }
  }
}

Direct Command Line

msbaseagent

Configuration

All database connection parameters are pre-configured:

• Server: queryms.ucsf.edu
• Port: 3306
• Username: medcp
• Password: Medcp_aiqueries_123#@!
• Database: imsms
• Namespace: MSAgent

No additional configuration is required!

Optional environment variable:

• MSBASE_LOG_LEVEL: Set logging level (DEBUG, INFO, WARNING, ERROR) - defaults to INFO

Available Tools

1. MSAgent-list_tables

List all tables in the MySQL database with their columns and data types.

Parameters:

• database (string, optional): Database name to list tables from (defaults to "imsms")

Example: Returns comprehensive schema information including table structure, column names, data types, constraints, and row counts.

2. MSAgent-execute_query

Execute a READ-ONLY SQL query on the UCSF MS medical database.

Parameters:

• query (string, required): SQL SELECT query to execute
• database (string, optional): Database name to execute query against (defaults to "imsms")

Example:

SELECT COUNT(*) FROM patients WHERE diagnosis_date > '2023-01-01'

Security

This server enforces read-only access to the MS database. Write operations (INSERT, UPDATE, DELETE, CREATE, DROP, ALTER, TRUNCATE, etc.) are not permitted.

Important:

• Only SELECT, SHOW, DESCRIBE, and EXPLAIN queries are allowed
• The database contains de-identified patient data
• Follow all UCSF data use policies and HIPAA regulations

Network Requirements

• UCSF Network Access: Must be connected to UCSF network or VPN
• Port 3306: MySQL port must be accessible
• DNS Resolution: Must be able to resolve queryms.ucsf.edu

Database Structure

The UCSF MS medical database contains clinical research data related to Multiple Sclerosis patients, including:

• Patient demographics
• Clinical assessments
• Treatment records
• Disease progression markers
• Lab results
• Imaging data

Use the MSAgent-list_tables tool to explore the complete database schema.

Troubleshooting

Database Connection Failed

• Check UCSF VPN connection
• Verify network connectivity to queryms.ucsf.edu
• Ensure port 3306 is accessible

Permission Denied

• Verify you are connected to UCSF network or VPN
• Check if database server is accessible
• Contact UCSF IT if issues persist

Query Errors

• Use MSAgent-list_tables to verify table and column names
• Check SQL syntax
• Ensure query is read-only (SELECT statements only)

License

MIT

Author

Wanjun Gu

• Email: wanjun.gu@ucsf.edu
• Website: https://broccolito.github.io/

About

MSBaseAgent is designed specifically for authorized medical research personnel at UCSF working with Multiple Sclerosis clinical data. It provides secure, read-only access to clinical databases for research analysis and data exploration.

Acknowledgments

• UCSF Multiple Sclerosis Center for database access
• Model Context Protocol (MCP) community
• FastMCP framework