SPOKEAgent

An MCP (Model Context Protocol) server for querying the SPOKE biomedical knowledge graph for rapid biomedical knowledge inference. Points to the official release of SPOKE.

BioRouter Extension

Download spokeagent.brxt

Drag the .brxt file into BioRouter's Extensions → Add extension dialog. BioRouter will install the virtual environment automatically and prompt for required credentials.

Variable	Required	Default	Description
SPOKEAGENT_PASSCODE	✅	—	Passcode from the SPOKEAgent credentials page

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

Alternative install (custom extension via uvx)

If you prefer not to use the .brxt bundle, you can register SPOKEAgent as a custom extension command:

1. In BioRouter, go to Add custom extension

2. Fill in the extension name and description

3. For the command, use the following:

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

4. Add an environment variable:

   a. Variable name = SPOKEAGENT_PASSCODE

   b. Value = <your-passcode> (from the credentials page)

   c. Click + Add to add the variable.

5. 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)

Editors

• Ilan Ladabaum (ilan.ladabaum@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.