# Cbioportal (npm · @pipeworx/mcp-cbioportal)

cBioPortal MCP — cancer genomics portal.

- Trust score: 84/100 (high trust)
- Change this week: +3
- Registry status: active
- Liveness: live
- Owner verified: no
- Last scored: 2026-11-05

## Components

- remote · `gateway.pipeworx.io`: 77/100, [markdown](https://verifymcp.io/servers/pipeworx-io-cbioportal/cbioportal-mcp.md), [page](https://verifymcp.io/servers/pipeworx-io-cbioportal/cbioportal-mcp)
- npm · `@pipeworx/mcp-cbioportal`: 84/100 (this document), [markdown](https://verifymcp.io/servers/pipeworx-io-cbioportal/pipeworx-mcp-cbioportal.md), [page](https://verifymcp.io/servers/pipeworx-io-cbioportal/pipeworx-mcp-cbioportal)

## Channel facts

- Registry: `npm`
- Package: `@pipeworx/mcp-cbioportal`
- Version: `0.2.1`
- Transport: `stdio`

## Trust breakdown

How this component scores in each security and reliability category. Every signal is checked automatically from public evidence about the published package, including repeated runs of it in an isolated sandbox, and we only credit what we can confirm. Scores are 0–100 per category. Scoring method: https://verifymcp.io/docs/scoring (what has changed: https://verifymcp.io/docs/scoring/changelog)

Scored 2026-11-05.

- **Supply Chain Security**: 100/100
  - No malware found by supply-chain analysis.
  - No known CVEs affecting this package version or its production dependencies.
  - No install/post-install scripts declared.
  - No production dependencies, so there is no dependency health to assess.
- **Provenance & Transparency**: 97/100
  - Source repository is publicly reachable at the declared URL.
  - Cryptographically verified build provenance (signed, bound to pipeworx-io/mcp-cbioportal).
  - Clear OSI-approved license (MIT).
  - Actively maintained (last published 5 days ago).
  - Disclosure check failed: no security disclosure policy was found in the source repository.
- **Schema Quality & AI Usability**: 77/100
  - AI-judged instruction clarity (good).
  - Tool/resource definitions use about 407 tokens (~101/item across 4 items; 4 tools + 0 resources), lean.
  - Usage-examples check failed: none of the tools include examples.
- **Stability & Change Management**: 23/100
  - Stability observed for 7 of 30 days with no destabilising changes; credit accrues until the full window elapses.
- **Tool Coverage**: 100/100
  - 100% of tools have a non-trivial description (not blank, and not just the tool's name).
  - 100% of tool parameters carry a description.
- **Tool Safety**: 100/100
  - No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.
  - We read all 4 captured tool definition(s), and no name or description among them implies an irreversible operation.
  - An AI judge read all 5 captured unit(s) of tool text and found none that tries to manipulate the model reading it.
- **Capabilities**: 100/100
  - Implements a supported MCP spec version (2025-11-25); the latest is 2026-07-28.

## Install

### How do I install the Cbioportal MCP server?

Cbioportal runs locally as an npm package, launched with npx -y @pipeworx/mcp-cbioportal. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.

### Claude

```bash
claude mcp add pipeworx-io-cbioportal -- npx -y @pipeworx/mcp-cbioportal
```

### Cursor

```json
{
  "mcpServers": {
    "pipeworx-io-cbioportal": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-cbioportal"
      ]
    }
  }
}
```

### VS Code

```json
{
  "servers": {
    "pipeworx-io-cbioportal": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-cbioportal"
      ]
    }
  }
}
```

### Codex

```bash
codex mcp add pipeworx-io-cbioportal -- npx -y @pipeworx/mcp-cbioportal
```

### opencode

```json
{
  "$schema": "https://opencode.ai/config.json",
  "mcp": {
    "pipeworx-io-cbioportal": {
      "type": "local",
      "command": [
        "npx",
        "-y",
        "@pipeworx/mcp-cbioportal"
      ],
      "enabled": true
    }
  }
}
```

### OpenClaw

```bash
openclaw mcp add pipeworx-io-cbioportal --command npx --arg -y --arg @pipeworx/mcp-cbioportal
```

### Hermes

```yaml
mcp_servers:
  pipeworx-io-cbioportal:
    command: "npx"
    args: ["-y", "@pipeworx/mcp-cbioportal"]
```

### Netclaw

```json
{
  "McpServers": {
    "pipeworx-io-cbioportal": {
      "Transport": "stdio",
      "Command": "npx",
      "Arguments": [
        "-y",
        "@pipeworx/mcp-cbioportal"
      ]
    }
  }
}
```

### Vellum

```bash
assistant mcp add pipeworx-io-cbioportal -t stdio -c npx -a -y @pipeworx/mcp-cbioportal
```

### Other

```json
{
  "mcpServers": {
    "pipeworx-io-cbioportal": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-cbioportal"
      ]
    }
  }
}
```

## Changelog

Every change recorded for this component, newest first. Days that predate change tracking, or that we cannot explain, say so: "we were watching and nothing happened" and "we were not watching" are different claims.

### 2026-11-03 (score 84, +1)

No change was recorded against any check on this day. Stability & Change Management went from 13 to 17. That category is still filling its 30-day observation window: 4 days of observed history at the previous scan, 5 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-11-01 (score 83, +1)

- [functional regression] Security disclosure: unverified → fail

### 2026-10-31 (score 82, 0)

- [functional regression] Security disclosure: fail → unverified
- [functional] Package version: 0.2.0 → 0.2.1

### 2026-10-30 (score 82, +1)

No change was recorded against any check on this day. Stability & Change Management went from 0 to 3. That category is still filling its 30-day observation window: 0 days of observed history at the previous scan, 1 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-10-29 (score 81)

First indexed and scored.

## MCP tools (4)

### `search_studies` (~127 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.

Input parameters:

- `limit` (number): Max studies to return (default 25, max 100).
- `query` (string): Keyword to match against study name / id / cancer type (e.g. "breast", "tcga", "glioma"). Omit to list studies.

### `get_study` (~81 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.

Input parameters:

- `study_id` (string, required): cBioPortal study id, e.g. "brca_tcga_pub".

### `get_gene` (~88 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.

Input parameters:

- `gene` (string, required): HUGO gene symbol (e.g. "TP53") or Entrez gene id.

### `list_cancer_types` (~57 tokens)

List cancer types defined in cBioPortal (id, display name, parent type). Useful for resolving cancer-type ids used by studies.

Input parameters:

- `limit` (number): Max cancer types to return (default 50, max 200).

## Diagnostics

Captured diagnostic sections: Provenance, Dependencies. The full working is on the page: https://verifymcp.io/servers/pipeworx-io-cbioportal/pipeworx-mcp-cbioportal#diagnostics

## Score history

- 2026-11-05: 84
- 2026-11-04: 84
- 2026-11-03: 84
- 2026-11-02: 83
- 2026-11-01: 83
- 2026-10-31: 82
- 2026-10-30: 82
- 2026-10-29: 81

## Common questions

### What is the Cbioportal MCP server?

Cbioportal is an MCP server listed in the public MCP registry as io.github.pipeworx-io/cbioportal. cBioPortal MCP, cancer genomics portal. This page covers its npm package (@pipeworx/mcp-cbioportal).

### Is the Cbioportal MCP server safe to use?

Cbioportal scores 84 out of 100 on VerifyMCP. We found no known CVEs affecting it as of 5 November 2026. It declares no install or post-install scripts. Its build provenance is signed and verified. That is a record of what we were able to check automatically, not an endorsement. The category breakdown on this page shows every signal behind the number, including the ones we could not confirm.

### What tools does the Cbioportal MCP server expose?

Cbioportal exposes 4 tools: search_studies, get_study, get_gene, list_cancer_types. Their descriptions and schemas cost roughly 353 tokens of context every time the server is loaded.

### Is the Cbioportal MCP server still maintained?

Cbioportal is still listed as active in the MCP registry. We last reached this channel on 5 November 2026. Those dates come from our own scans of the registry and the channel itself, not from anything the publisher announced.

### What licence is the Cbioportal MCP server under?

Cbioportal declares the MIT licence, which is OSI-approved. That covers the source only, and says nothing about the cost of any service it calls.

### What did VerifyMCP test on the Cbioportal MCP server?

VerifyMCP ran 16 checks on Cbioportal, covering Malware scan, Known CVEs, Install scripts, Dependency health and 12 more. Endpoint Security and Transport & Reachability do not apply to an npm package, so they were not tested. The score does not measure everything, and the scoring documentation lists what it leaves out.

## Links

- npm package: https://www.npmjs.com/package/@pipeworx/mcp-cbioportal
- Socket report: https://socket.dev/npm/package/@pipeworx/mcp-cbioportal
- Repository: https://github.com/pipeworx-io/mcp-cbioportal
- Website: https://pipeworx.io/packs/cbioportal
- Changelog RSS feed: https://verifymcp.io/servers/pipeworx-io-cbioportal/pipeworx-mcp-cbioportal.xml
- Changelog JSON feed: https://verifymcp.io/servers/pipeworx-io-cbioportal/pipeworx-mcp-cbioportal/changelog.json
- Trust report (JSON): https://verifymcp.io/servers/pipeworx-io-cbioportal/pipeworx-mcp-cbioportal.json
- HTML version of this page: https://verifymcp.io/servers/pipeworx-io-cbioportal/pipeworx-mcp-cbioportal