AACT Clinical Trials MCP Server

Query the AACT (ClinicalTrials.gov) database directly from Claude. Explore 70+ tables of clinical trial data — studies, interventions, outcomes, sponsors, facilities — using read-only SQL with buffered pagination.

Why AACT over the ClinicalTrials.gov API?

The ClinicalTrials.gov API returns one JSON record per trial — useful for quick lookups, but awkward for analytics. Want the average duration of Phase 2 NSCLC trials from 2020-2025? With the API you'd filter trials, extract dates from each JSON record, then compute durations client-side. With AACT, that's a single SQL query.

A structured PostgreSQL database makes it far easier to aggregate, combine, and summarize clinical trial data in any way you need. And for AI-assisted analysis, SQL is a standard that LLMs handle extremely well — fewer mistakes, less context to manage, better performance, and lower cost compared to parsing bespoke API responses.

Note: This is an independent, third-party integration. It is not affiliated with or endorsed by the Clinical Trials Transformation Initiative (CTTI) or Duke University. However, we released a case study with CTTI on integrating their database with Claude - see AACT case study.

Tools

Tool	Description
database_info	Confirm database connection, server time, and data currency
list_tables	Discover all available tables with approximate row counts
describe_table	Inspect column names, types, distinct counts, and sample values
get_column_values	Get distinct values for a column with counts — essential before filtering
search_columns	Find columns by keyword across all tables (e.g. masking -> designs.masking)
read_query	Execute a SELECT, CTE, or EXPLAIN query with buffered results and preview
fetch_rows	Page through buffered query results without re-querying

All tables join on nct_id.

Setup

1. Create a free account at https://aact.ctti-clinicaltrials.org/users/sign_up
2. Install the plugin (see options below)
3. Enter your AACT credentials when prompted

Installation

Option 1: Claude Desktop Plugin (recommended)

Download the latest .mcpb file from Releases and open it in Claude Desktop. You'll be prompted for your AACT credentials.

Option 2: Published package

Add to your claude_desktop_config.json (~/Library/Application Support/Claude/claude_desktop_config.json on macOS, %APPDATA%\Claude\claude_desktop_config.json on Windows):

{
  "mcpServers": {
    "aact": {
      "command": "uvx",
      "args": ["mcp-server-aact"],
      "env": {
        "DB_USER": "your_username",
        "DB_PASSWORD": "your_password"
      }
    }
  }
}

Option 3: Docker

{
  "mcpServers": {
    "aact": {
      "command": "docker",
      "args": [
        "run", "--rm", "-i",
        "--env", "DB_USER=your_username",
        "--env", "DB_PASSWORD=your_password",
        "navisbio/mcp-server-aact:latest"
      ]
    }
  }
}

Option 4: From source

git clone https://github.com/navisbio/mcp-server-aact.git
cd mcp-server-aact
uv sync

{
  "mcpServers": {
    "aact": {
      "command": "uv",
      "args": ["run", "--directory", "/path/to/mcp-server-aact", "mcp-server-aact"],
      "env": {
        "DB_USER": "your_username",
        "DB_PASSWORD": "your_password"
      }
    }
  }
}

Example Prompts

1. Competitive landscape analysis

"Who are the top 10 sponsors of Phase 3 Alzheimer's disease trials? Break down by trial status."

The server will discover relevant tables, check enum values for phase and status, then build a query joining studies, conditions, and sponsors.

2. Drug pipeline search

"Find all actively recruiting Phase 2 and Phase 3 trials for pembrolizumab in non-small cell lung cancer. Show NCT ID, title, enrollment, and lead sponsor."

Uses get_column_values to confirm phase format (PHASE2, PHASE3), then queries across studies, browse_interventions, and conditions.

3. Endpoint analysis

"What are the most common primary outcome measures in completed Phase 3 type 2 diabetes trials?"

Joins studies with outcomes to analyze endpoint patterns, grouped by outcome measure type.

4. Geographic distribution

"How many clinical trial sites does a typical rare disease trial have? Show the top countries by site count."

Queries the facilities table joined with conditions to map trial geography.

Privacy

This server is read-only and does not collect or store any personal data. See PRIVACY.md for details.

Troubleshooting

Connection or authentication errors

• Verify your AACT credentials at https://aact.ctti-clinicaltrials.org/users/sign_in
• The AACT database undergoes weekly maintenance (typically weekends) — try again later if the connection is refused
• Ensure DB_USER and DB_PASSWORD are set correctly in your config

spawn uvx ENOENT error

The system cannot find uvx. Use the full path:

{
  "mcpServers": {
    "aact": {
      "command": "/Users/username/.local/bin/uvx",
      "args": ["mcp-server-aact"],
      "env": {
        "DB_USER": "your_username",
        "DB_PASSWORD": "your_password"
      }
    }
  }
}

Contributing

• Open an issue on GitHub
• Email: jonas.walheim@navis-bio.com

License

MIT