MCP server

Cbioportal

io.github.pipeworx-io/cbioportal

Checked 26 Oct 2026, 08:29 UTC · Connected to it and listed its tools

cBioPortal MCP — cancer genomics portal.

From the maker's README Part of Pipeworx — an MCP gateway connecting AI agents to 1875+ live data sources. This is an independent, unofficial integration — not affiliated with, endorsed by, or published by the upstream provider. Source

Website Source

At a glance

Type

MCP server

Publisher

pipeworx.io (verified by the MCP Registry)

Status

Working at last check

Tools

46

Token cost

About 26,825 tokens per request

Sets up in

Claude Code, Claude Desktop, Codex, Gemini CLI, Cursor, VS Code, Antigravity, ChatGPT, OpenAI API, Grok

Last checked

26 Oct 2026, 08:29 UTC

Connect it to your agent

Add to CursorAdd to VS CodeVS Code Insiders

Opens the app, which shows the server and asks you to confirm. For other apps, copy the setup below.

Claude Code

claude mcp add --transport http cbioportal https://gateway.pipeworx.io/cbioportal/mcp

Claude Desktop

Settings → Connectors → Add custom connector, and paste the URL.

Codex (config.toml)

[mcp_servers.cbioportal]
url = "https://gateway.pipeworx.io/cbioportal/mcp"

Gemini CLI

{"mcpServers":{"cbioportal":{"httpUrl":"https://gateway.pipeworx.io/cbioportal/mcp"}}}

Cursor

{"mcpServers":{"cbioportal":{"url":"https://gateway.pipeworx.io/cbioportal/mcp"}}}

VS Code

{"servers":{"cbioportal":{"type":"http","url":"https://gateway.pipeworx.io/cbioportal/mcp"}}}

Antigravity

agy mcp add cbioportal https://gateway.pipeworx.io/cbioportal/mcp

ChatGPT

Settings → Apps & Connectors → Advanced settings: turn on Developer mode, then Create a connector and paste the URL. Which plans can do this varies.

OpenAI API (Responses tools)

{"type":"mcp","server_label":"cbioportal","server_url":"https://gateway.pipeworx.io/cbioportal/mcp","require_approval":"always"}

Grok (xAI API tools)

{"type":"mcp","server_label":"cbioportal","server_url":"https://gateway.pipeworx.io/cbioportal/mcp"}

Tools

• get_gene ~122 tokens
  Resolve a gene to its Entrez gene id and canonical info via cBioPortal. Accepts a HUGO symbol (e.g. "TP53", "BRCA1") or an Entrez gene id. Returns entrez_gene_id, symbol, and type.
• get_study ~122 tokens
  Get full details for one cBioPortal cancer study by its study id (e.g. "brca_tcga_pub", "glioma_mskcc_2019"), including description, cancer type, sample count, PMID, and citation.
• list_cancer_types ~97 tokens
  List cancer types defined in cBioPortal (id, display name, parent type). Useful for resolving cancer-type ids used by studies.
• search_studies ~181 tokens
  Search public cancer genomics studies in cBioPortal (TCGA, CPTAC, MSK, etc.) by keyword. Matches study name, study id, or cancer-type id (case-insensitive). Returns study ids, names, cancer types, and sample counts. Keyless, open data.

Browse

• GitHub tools
• GitHub and code hosting
• Government and public data

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