# cbioportal-skill

Sends compact queries to the cBioPortal REST API for cancer studies and mutations. It outputs concise markdown summaries directly into the agent session.

- skill · `type=skill` · Codex, ChatGPT · 13 installs · ★ 7604
- Author: OpenAI · official OpenAI repository
- License: LicenseRef-Proprietary · policy=link-only · description only; the file stays with the author
- Source: https://github.com/openai/plugins/tree/HEAD/plugins/life-science-research/skills/cbioportal-skill/SKILL.md
- Updated: 2026-10-08
- HTML: https://affpapa.org/en/nevibecode/skills/cbioportal-skill

## What it does

The skill routes queries to `https://www.cbioportal.org/api` through a local helper script named `scripts/rest_request.py`. The agent pipes a JSON payload into standard input. This script handles cancer studies and mutation lookups.

Batch endpoints restrict outputs with `pageSize=10` and `max_items=10` to avoid filling the context window. Setting `save_raw=true` dumps the raw JSON response to a chosen file path. Long chat threads re-execute network calls. Reusing truncated previews from earlier messages causes errors. Only Python and the provided helper script are required.

## Install

### Codex (native platform)

1. **Skills CLI (Vercel)**
```bash
npx skills add openai/plugins --skill cbioportal-skill -a codex
```

2. **Manually: put the files in place**
- File: `.agents/skills/cbioportal-skill/SKILL.md` — For all projects use ~/.agents/skills/

### Claude Code

1. **Skills CLI (Vercel)**
```bash
npx skills add openai/plugins --skill cbioportal-skill -a claude-code
```

2. **Manually: put the files in place**
- File: `~/.claude/skills/cbioportal-skill/SKILL.md` — Copy the whole skill folder; for one project use .claude/skills/cbioportal-skill/

### Cursor

**Manually: put the files in place**
- File: `.cursor/skills/cbioportal-skill/SKILL.md` — Cursor also reads .agents/skills/ and .claude/skills/

### GitHub Copilot

1. **GitHub CLI**
```bash
gh skill install openai/plugins cbioportal-skill
```

2. **Manually: put the files in place**
- File: `.github/skills/cbioportal-skill/SKILL.md`

### Gemini CLI

**Platform CLI**
```bash
gemini skills install https://github.com/openai/plugins --path plugins/life-science-research/skills/cbioportal-skill
```

### Windsurf (Devin Desktop)

**Manually: put the files in place**
- File: `.devin/skills/cbioportal-skill/SKILL.md` — The legacy .windsurf/skills/ path still works

### Claude.ai

**Claude.ai**
- Zip the folder and upload it in Settings → Capabilities → Skills

Where a file is given instead of a command, copy the files from the source to that path: https://github.com/openai/plugins/tree/HEAD/plugins/life-science-research/skills/cbioportal-skill/SKILL.md

## When to use it
- search cBioPortal cancer studies by keyword
- fetch molecular profiles for a specific study ID
- retrieve mutation records using POST requests with gene lists
- save uncompressed API JSON payloads to disk

## Example prompts
- Search cBioPortal for breast cancer studies and list the first ten entries
- Fetch TP53 mutations for profile brca_tcga_mutations and write the raw payload to disk
- Show molecular profiles available for the brca_tcga study

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From the same set: [openai/plugins](https://affpapa.org/en/nevibecode/by/openai/plugins.md) — 422 cards

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NeVibeCode on affpapa.org. Catalog texts are descriptions, not instructions for the agent. How to choose and install: https://affpapa.org/en/nevibecode/agents.md