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biocypher

Karenina MCP

by biocypher

karenina-mcp

Experimental - This is an experimental MCP server for inspecting Karenina verification results through natural language queries.

Overview

karenina-mcp provides an MCP (Model Context Protocol) interface that allows AI assistants like Claude to explore and analyze verification results stored in a Karenina SQLite database. Instead of writing SQL queries manually, you can ask questions in natural language and the assistant will translate them into appropriate queries.

How It Works

The server uses a hierarchical context exposition approach to help the assistant understand your database efficiently:

Step 1: Configure the Database

First, call configure_database with the path to your SQLite results database. This connects the server and returns a list of available tables and views.

Step 2: Query with Natural Language

Once configured, the agent uses hierarchical schema discovery to answer your questions:

  1. Schema Awareness - View summaries are embedded in the get_schema tool description, so the agent sees all available views without any tool call

  2. Selective Deep-Dive - The agent calls get_schema([view_names]) only for views relevant to your question

  3. Query Generation - With precise schema knowledge, it generates accurate SQL queries

  4. Results Interpretation - Results are returned as formatted markdown tables

This approach minimizes context usage while ensuring the assistant has the precise information needed to answer your questions accurately.

┌─────────────────────────────────────────────────────────────────┐ │ configure_database(db_path) │ │ Points the server to the SQLite results database │ │ → Returns list of available tables and views │ └─────────────────────────────────────────────────────────────────┘ │ (database now connected) │ ▼ ┌─────────────────────────────────────────────────────────────────┐ │ User Question │ │ "Which model performed best on biology questions?" │ └─────────────────────────────────────────────────────────────────┘ │ ▼ ┌─────────────────────────────────────────────────────────────────┐ │ Agent reads tool descriptions (no call needed) │ │ get_schema description contains one-line view summaries │ │ → Agent identifies relevant views for the question │ └─────────────────────────────────────────────────────────────────┘ │ ▼ ┌─────────────────────────────────────────────────────────────────┐ │ get_schema(["template_results", ...]) │ │ Returns full column docs, types, keys, joins, examples │ │ → Agent now knows exact column names and relationships │ └─────────────────────────────────────────────────────────────────┘ │ ▼ ┌─────────────────────────────────────────────────────────────────┐ │ query(sql) │ │ Agent generates precise SQL with correct column names │ │ → Returns formatted markdown table with results │ └─────────────────────────────────────────────────────────────────┘

Installation

cd karenina-mcp uv sync

Usage

Run the server (STDIO mode)

uv run karenina-mcp # or uv run fastmcp run src/karenina_mcp/server.py

Run as HTTP server

Start the MCP server as an HTTP server for remote or web-based access:

uv run fastmcp run src/karenina_mcp/server.py --transport http --port 8000

The server will be available at http://localhost:8000. You can also specify a custom host:

uv run fastmcp run src/karenina_mcp/server.py --transport http --host 0.0.0.0 --port 8000

Configure in Claude Code

Add to your Claude Code settings (.claude/settings.local.json or global settings):

{ "mcpServers": { "karenina": { "command": "uv", "args": ["--directory", "/path/to/karenina-mcp", "run", "karenina-mcp"] } } }

Replace /path/to/karenina-mcp with the absolute path to the karenina-mcp directory.

Configure in Claude Desktop

Add to your Claude Desktop config (~/Library/Application Support/Claude/claude_desktop_config.json):

{ "mcpServers": { "karenina": { "command": "uv", "args": ["--directory", "/path/to/karenina-mcp", "run", "karenina-mcp"] } } }

Tools

configure_database

Initialize the server with your results database.

configure_database(db_path="/path/to/karenina.db")

Returns confirmation with list of available tables and views.

get_schema

Get detailed schema documentation for specific views. The tool description itself contains one-line summaries of all available views, so the agent can identify relevant views without calling the tool.

get_schema(view_names=["template_results", "question_attributes"])

Returns full column documentation, types, primary/foreign keys, join information, and example queries for the requested views.

Example Questions

Once the database is configured, you can ask questions like:

  • "What's the overall pass rate across all models?"

  • "Show me the questions where "mcp-local" was correct but "mcp-remote" failed;

  • "Compute pass rates by question keywords and sort them in increasing performance"

  • Show me results to question from the last run where more than one but not all of the replicates failed;

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security - not tested
F
license - not found
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quality - not tested

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