SPOKEAgent

An MCP (Model Context Protocol) server for querying the SPOKE biomedical knowledge graph for rapid biomedical knowledge inference.

Features

• Query SPOKE Knowledge Graph: Execute Cypher queries on the SPOKE biomedical knowledge graph
• Get SPOKE Schema: Retrieve the complete schema of the SPOKE knowledge graph including nodes, relationships, and properties
• Pre-configured Access: All SPOKE connection parameters are pre-configured - no setup required!

Installation

From GitHub (using uvx)

uvx --from git+https://github.com/Broccolito/SPOKEAgent spokeagent

Local Installation

cd SPOKEAgent
pip install -e .

Usage

As an MCP Server

Add to your MCP client configuration (e.g., Claude Desktop):

{
  "mcpServers": {
    "spokeagent": {
      "command": "uvx",
      "args": ["--from", "git+https://github.com/Broccolito/SPOKEAgent", "spokeagent"]
    }
  }
}

Direct Command Line

spokeagent

Configuration

All SPOKE connection parameters are pre-configured:

• URI: bolt://spokedev.cgl.ucsf.edu:7687
• Username: neo4j
• Password: SPOKEdev
• Database: spoke

No additional configuration is required!

Optional environment variable:

• SPOKE_LOG_LEVEL: Set logging level (DEBUG, INFO, WARNING, ERROR) - defaults to INFO

Available Tools

1. query_spoke

Execute a read-only Cypher query on the SPOKE biomedical knowledge graph.

Parameters:

• cypher_query (string, required): The Cypher query for biomedical knowledge inference
• parameters (dict, optional): Parameters to pass to the SPOKE query

Example:

MATCH (d:Disease)-[r:ASSOCIATES_DaG]->(g:Gene)
WHERE d.name = "Alzheimer's disease"
RETURN g.name, r.score
LIMIT 10

2. get_spoke_schema

List all nodes, their attributes, and their relationships in the SPOKE biomedical knowledge graph.

Returns: Complete schema including node types, properties, and relationships.

Security

This server enforces read-only access to the SPOKE knowledge graph. Write operations (CREATE, MERGE, DELETE, etc.) are not permitted.

License

MIT

Authors

• Wanjun Gu (wanjun.gu@ucsf.edu)
• Gianmarco Bellucci (gianmarco.bellucci@ucsf.edu)

About SPOKE

SPOKE (Scalable Precision medicine Oriented Knowledge Engine) is a large-scale biomedical knowledge graph that integrates data from multiple sources to support precision medicine research.