health-memex

Personal health data archive: consolidate medical records from multiple EHR systems into a single queryable SQLite database. Part of the *-memex ecosystem.

Query, analyze, and export your aggregated clinical data via CLI, MCP server (for LLM-assisted analysis), or self-contained HTML SPA.

Features

• Multi-EHR data consolidation: Import from Epic MyChart, MEDITECH Expanse, and athenahealth
• SQLite database: 17 clinical tables with full audit trail
• MCP server: 31 tools for LLM-assisted analysis with Claude
• Export formats: Self-contained HTML SPA, Arkiv (JSONL + README.md + schema.yaml)
• AI chat: Ask questions about your record in the HTML SPA via Claude, with inline charts (optional, requires proxy)
• Visit prep: See what's new since your last visit, directly in the SPA
• Print summary: One-page printable view for your doctor
• Personal notes: Tag and annotate any clinical record

Installation

pip install health-memex

# With MCP server support (for Claude integration)
pip install "health-memex[mcp]"

Development Setup

git clone https://github.com/queelius/health-memex.git
cd health-memex
pip install -e ".[dev,mcp]"

Quick Start

Load Data from EHR Exports

# Load from individual sources
health-memex load epic ~/exports/epic/
health-memex load meditech ~/exports/meditech/
health-memex load athena ~/exports/athena/

# Or load all at once
health-memex load all \
  --epic-dir ~/exports/epic/ \
  --meditech-dir ~/exports/meditech/ \
  --athena-dir ~/exports/athena/

Query and Inspect

# View database summary
health-memex summary

# Run SQL queries
health-memex query "SELECT test_name, value, result_date FROM lab_results ORDER BY result_date DESC LIMIT 10"

# What's new since your last visit
health-memex diff 2025-01-01

Export Your Data

# Self-contained HTML SPA with embedded SQLite (all data stays client-side)
health-memex export html --output summary.html
health-memex export html --output summary.html --embed-images --config health_memex.toml
health-memex export html --output summary.html --ai-chat --proxy-url https://proxy.example.com/v1/messages

# Arkiv universal record format (primary backup/restore, round-trip capable)
health-memex export arkiv --output ./arkiv/
health-memex export arkiv --output ./arkiv/ --embed

# Import from arkiv archive
health-memex import ./arkiv/ --db new.db
health-memex import ./arkiv/ --validate-only

MCP Server

# Start MCP server (matches ecosystem pattern: memex mcp, btk mcp)
health-memex mcp --db health_memex.db

Claude Code Configuration

{
  "mcpServers": {
    "health-memex": {
      "command": "python",
      "args": ["-m", "health_memex", "mcp", "--db", "/path/to/health_memex.db"]
    }
  }
}

Personal Notes

health-memex notes list --limit 20
health-memex notes search --tag oncology --query "CEA"

Supported EHR Sources

Database Schema

17 clinical tables, all dates ISO YYYY-MM-DD, every record carries a source field:

Configuration

health-memex init-config

Generates health_memex.toml with lab tests to chart based on what's in your database.

Requirements

• Python 3.11+
• Dependencies: lxml, pyyaml
• Optional: mcp (FastMCP) for MCP server

License

MIT