AI Chat with Medical Data MCP Servers

Learn to interact with AI assistants using real-world medical and pharmaceutical data through Model Context Protocol (MCP) servers.

What You'll Learn

1. Interact with AI Chat in VSCode - Use GitHub Copilot Chat with specialized MCP servers
2. Query PubMed - Search and analyze medical literature using natural language
3. Access FDA Data - Query drug information, adverse events, recalls, and medical device data

Quick Start

1. Launch in Codespaces

Click the "Open in GitHub Codespaces" button above or:

1. Fork this repository
2. Click the green "Code" button
3. Select "Create codespace on main"

The environment will automatically set up with:

• Python 3.11
• Node.js 20
• GitHub Copilot extensions
• Both MCP servers (PubMed and OpenFDA)

2. Add MCP Servers

After the Codespace launches, add the MCP servers through VS Code:

1. Open Command Palette: Press Ctrl+Shift+P (Windows/Linux) or Cmd+Shift+P (macOS)

2. Run Add MCP Server: Type MCP: Add MCP Server and select the command

3. Choose Connection Type: Select stdio

4. Add PubMed Server:

   • Command: bash
   • Args: -c "source /workspaces/CC/mcp-servers/pubmearch/.venv/bin/activate && python -m pubmearch.server"
   • Target: Workspace

5. Add OpenFDA Server:

   • Command: bash
   • Args: -c "node /workspaces/CC/mcp-servers/OpenFDA-MCP-Server/build/index.js"
   • Target: Workspace

3. Configure API Keys

Create a .env file from the template:

cp .env.example .env

Edit .env and add your API keys:

# PubMed API (Required)
export NCBI_USER_EMAIL="your_email@example.com"
export NCBI_USER_API_KEY="your_api_key"

# FDA API (Optional - increases rate limit)
export FDA_API_KEY="your_fda_key"

Getting API Keys

PubMed API Key (Required):

1. Go to NCBI Account Settings
2. Log in or create an account
3. Scroll to "API Keys" section
4. Click "Create API Key"

FDA API Key (Optional - increases rate limit from 1,000 to 120,000 requests/hour):

1. Visit openFDA Authentication
2. Sign up for an API key

4. Start Using AI Chat

Open GitHub Copilot Chat (Ctrl+Shift+I or Cmd+Shift+I) and try these example prompts.

Tip: Use #pubmed or #openfda at the start of your message to tell the AI which MCP server to use.

PubMed Research Examples

#pubmed Find recent studies about diabetes treatment

#pubmed What are the latest papers on Alzheimer's disease?

#pubmed Show me research trends for COVID-19 vaccines

#pubmed Search for studies about heart disease prevention published in the last year

#pubmed Find papers about cancer immunotherapy from 2024

#pubmed What's the latest research on obesity and mental health?

#pubmed Search for studies comparing different diabetes medications

#pubmed Find research about sleep disorders and their treatments

FDA Drug & Device Examples

#openfda Find side effects reported for ibuprofen

#openfda What adverse events have been reported for insulin?

#openfda Show me recent drug recalls

#openfda Find all FDA-approved medications for high blood pressure

#openfda What drugs were recalled due to contamination?

#openfda Search for adverse events related to pacemakers

#openfda Find information about diabetes medications made by Novo Nordisk

#openfda What are the reported side effects of aspirin?

#openfda Show me drug shortages for antibiotics

#openfda Find recalls of medical devices in the last 6 months

MCP Servers Included

1. PubMed MCP Server

Query and analyze medical literature from PubMed.

Features:

• Literature search with advanced syntax
• Research hotspot analysis
• Trend tracking over time
• Publication count statistics
• Comprehensive reports

Tools Available:

• search_pubmed - Search PubMed database
• analyze_research_keywords - Identify research hotspots
• analyze_publication_count - Track publication trends
• generate_comprehensive_analysis - Full analysis reports

2. OpenFDA MCP Server

Access FDA databases for drugs and medical devices.

Features:

• Drug adverse event reports (FAERS)
• Drug labeling information
• Drug recalls and shortages
• FDA-approved drugs database
• Medical device data (510k, classifications, adverse events)

Tools Available:

• search_drug_adverse_events - FAERS data
• search_drug_labels - Product labeling
• search_drug_ndc - National Drug Code directory
• search_drug_recalls - Recall enforcement
• search_drugs_fda - FDA-approved drugs
• search_drug_shortages - Current shortages
• search_device_510k - Device clearances
• search_device_adverse_events - Device adverse events

Project Structure

.
├── .devcontainer/          # Codespaces configuration
│   ├── devcontainer.json   # Container settings
│   └── post-create.sh      # Setup script
├── .vscode/
│   └── mcp.json            # MCP server configuration
├── .env.example            # API keys template
├── .env                    # Your API keys (create from template)
├── mcp-servers/            # MCP server installations (auto-generated)
│   ├── pubmearch/          # PubMed MCP server
│   └── OpenFDA-MCP-Server/ # FDA MCP server
└── README.md               # This file

Advanced Usage

Using PubMed Advanced Search Syntax

PubMed supports advanced search queries:

# Search in specific fields
diabetes[Title/Abstract]

# Combine terms
(prostat*[Title/Abstract]) AND (cancer[Title/Abstract]) AND (immuno*[Title/Abstract])

# Date ranges
cancer[Title] AND ("2023/01/01"[PDAT] : "2023/12/31"[PDAT])

Filtering FDA Queries

FDA queries support detailed filtering:

Find drug adverse events for:
- Drug: aspirin
- Country: United States
- Date range: 2023-01-01 to 2023-12-31
- Serious events only: true

Generating Reports

Both MCP servers can generate comprehensive analysis reports:

Generate a comprehensive analysis of COVID-19 vaccine research from the past 6 months

Troubleshooting

API Key Issues

Problem: "Authentication failed" or "Rate limit exceeded"

Solution:

1. Verify .env file exists and contains correct API keys
2. For PubMed, ensure both NCBI_USER_EMAIL and NCBI_USER_API_KEY are set
3. Save the file - changes take effect immediately

MCP Server Not Responding

Problem: Chat doesn't recognize PubMed/FDA queries

Solution:

1. Check .env file exists with your API keys
2. Verify the MCP servers were installed:

   ls -la mcp-servers/

3. Try using the #pubmed or #openfda prefix in your message

Learning Resources

• Model Context Protocol Documentation
• PubMed Search Tips
• OpenFDA API Documentation
• GitHub Copilot Chat Documentation

Credits

• PubMed MCP Server: darkroaster/pubmearch
• OpenFDA MCP Server: Augmented-Nature/OpenFDA-MCP-Server

License

This educational project is provided as-is for learning purposes.

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Note: This tool provides access to public medical datasets. Always consult healthcare professionals for medical decisions and drug information.