Model Context Protocol (MCP)

This document provides technical information about the Model Context Protocol (MCP) servers and architecture that power AI integrations with cBioPortal.

Note: The cBioPortal MCP servers power the live cBioPortalChat interface and remain in active development, so their interfaces may still change.

What is MCP?

The Model Context Protocol (MCP) is a standard protocol that enables AI assistants to interact with external data sources and tools. MCP servers act as bridges between AI models (like Claude) and databases, APIs, or other services, allowing the AI to access and query data in a structured way.

For details on how MCP powers the cBioPortal chat interface, see the Chat Interface documentation.

Available MCP Servers

cBioPortal MCP Servers

The live cBioPortalChat bot is a single agent that uses both of the cBioPortal MCP servers below at the same time — it is one bot with two MCP servers:

cbioportal-mcp powers the database-query capability (referred to as the "database MCP" in the Chat Interface documentation).
cbioportal-navigator powers the link-generation capability (the "navigator MCP").

The agent decides which of the two to call for each turn. Both servers are developed by the cBioPortal team and remain in active development.

cbioportal-mcp

A specialized MCP server that wraps the ClickHouse database connection with cBioPortal-specific knowledge.

Repository: https://github.com/cBioPortal/cbioportal-mcp

Key Features:

Wraps the mcp-clickhouse server for ClickHouse database connectivity
Includes cBioPortal-specific system prompts that teach the AI about cancer genomics data structures
Enables natural language queries against cBioPortal's ClickHouse database
Supports multiple deployment options (development mode, Docker)
Includes MCP Inspector for debugging and monitoring

How it works: The server acts as an intermediary that combines ClickHouse database access with domain-specific instructions, allowing researchers and clinicians to query complex genomic datasets through conversational interfaces without writing SQL directly.

Backing data store: The server queries the ClickHouse database for AI agents. It has direct access to the same database tables used by the cBioPortal web application. See the ClickHouse Setup Guide to set one up.

Configuration: Uses environment variables for ClickHouse connection details and supports different transport protocols (stdio, HTTP, SSE).

cbioportal-navigator

An MCP server that enables AI agents to navigate and interact with the cBioPortal web interface.

Repository: https://github.com/fuzhaoyuan/cbioportal-navigator

Key Features:

Provides tools for navigating the cBioPortal website
Enables AI agents to interact with the web interface programmatically
Supports automated exploration of cBioPortal's web-based features

Community MCP Integrations

These integrations are maintained by the community and third-party developers.

BioMCP - cBioPortal Integration

An MCP integration that enhances biomedical literature searches with cBioPortal genomic data. When searching for articles with gene parameters, BioMCP automatically queries cBioPortal alongside PubMed searches, enriching results with mutation frequency and distribution data across cancer studies.

Maintainer: BioMCP community

Website: https://biomcp.org/backend-services-reference/03-cbioportal/

For more details on features and technical implementation, see the official BioMCP documentation.

Building Your Own MCP Integration

To build an MCP integration with cBioPortal:

Contact the community via Google Group or Slack to discuss your approach
Access data through:
- REST API - Programmatic access
- DataHub - Bulk data downloads
- ClickHouse database - Direct queries (not publicly accessible; contact us to discuss options). For details on setting up ClickHouse for your own MCP deployment, see the ClickHouse Setup Guide.