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

Access

SPOKEAgent is currently available to UCSF affiliates only.

To run the server, you will need a passcode (SPOKEAGENT_PASSCODE). Log in with your UCSF credentials at the link below to retrieve it:

SPOKEAgent Credentials (UCSF affiliates)

That page will show you how to set the environment variable and run the server.

Usage

SPOKEAgent is designed to be used with BioRouter. To add it:

1. In BioRouter, go to Add custom extension
2. Fill in the extension name and description
3. For the one-liner command, use the following (replacing <your-passcode> with the value from the credentials page above):

SPOKEAGENT_PASSCODE=<your-passcode> uvx --from git+https://github.com/Broccolito/SPOKEAgent spokeagent

1. Click Add extension — you're ready to go

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.