medical-research-mcp-suite: Instructions file for Claude Code

CLAUDE.md - AI Assistant Guide for Medical Research MCP Suite

Project Overview

This is a Model Context Protocol (MCP) server that provides AI-enhanced access to medical research databases. It unifies three major data sources:

• ClinicalTrials.gov - 400,000+ clinical studies
• PubMed - 35M+ research papers
• FDA Database - 80,000+ drug products and safety data

The server enables AI assistants (like Claude Desktop) to search, analyze, and correlate data across these databases.

Quick Reference

# Install dependencies
npm install

# Build TypeScript
npm run build

# Run MCP server (for Claude Desktop integration)
npm run dev

# Run web API server
npm run web

# Run tests
npm test

# Lint code
npm run lint

Architecture

src/
├── index.ts                    # Main MCP server entry point
├── web-server.ts               # Express web server (alternative to MCP)
├── apis/                       # External API clients
│   ├── clinicalTrials.ts       # ClinicalTrials.gov API client
│   ├── pubmed.ts               # PubMed/NCBI eUtils client
│   ├── fda.ts                  # openFDA API client
│   └── index.ts                # API exports
├── services/                   # Cross-database analysis services
│   ├── researchAnalyzer.ts     # Comprehensive drug/condition analysis
│   ├── drugSafety.ts           # Drug safety profile generation
│   ├── searchRefinementService.ts # Query refinement helpers
│   └── configurable-services.ts
├── types/                      # TypeScript type definitions
│   ├── index.ts                # Type exports
│   ├── common.ts               # Shared types
│   └── refinementTypes.ts      # Refinement-related types
├── config/                     # Configuration
│   ├── index.ts
│   └── public-interfaces.ts
└── utils/                      # Utility modules
    ├── cache.ts                # In-memory caching
    ├── logger.ts               # Winston logging
    ├── validators.ts           # Input validation
    ├── responseSizeMonitor.ts  # Response size limits for MCP
    ├── progressiveLoader.ts    # Paginated data loading
    ├── query-enhancer.ts       # Medical query enhancement
    └── drug-knowledge-graph.ts # Drug relationship mapping

tests/
└── clinicalTrials.test.ts      # Jest integration tests