# biobankjapan-phewas-skill

Retrieves single-variant BioBank Japan PheWAS summaries from rsID, GRCh37, or GRCh38 inputs. Useful for rapid genetic association checks inside your coding agent.

- 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/biobankjapan-phewas-skill/SKILL.md
- Updated: 2026-10-08
- HTML: https://affpapa.org/en/nevibecode/skills/biobankjapan-phewas-skill

## What it does

The skill operates by calling `scripts/biobankjapan_phewas.py` through standard input. It expects a JSON object containing exactly one variant key: `rsid`, `grch37`, `grch38`, or `variant`. Before contacting BioBank Japan, it normalizes coordinates into the required GRCh37 `chr:pos-ref-alt` string.

Responses render as compact Markdown summaries by default. The tool recommends starting with `max_results=10` to avoid consuming unnecessary context tokens. Whenever the complete dataset is needed, setting `save_raw=true` writes raw records to disk and reports the file location via `raw_output_path`.

Execution requires a local Python runtime alongside the `scripts/biobankjapan_phewas.py` helper script.

## Install

### Codex (native platform)

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

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

### Claude Code

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

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

### Cursor

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

### GitHub Copilot

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

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

### Gemini CLI

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

### Windsurf (Devin Desktop)

**Manually: put the files in place**
- File: `.devin/skills/biobankjapan-phewas-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/biobankjapan-phewas-skill/SKILL.md

## When to use it
- Retrieve BioBank Japan PheWAS summary statistics for a given rsID
- Map GRCh38 genomic coordinates to canonical GRCh37 before querying BBJ
- Export large association arrays to disk without overflowing context
- Inspect variant-phenotype links directly within an agent terminal

## Example prompts
- Look up BioBank Japan PheWAS associations for rs7903146 with the first 10 hits
- Query BBJ for GRCh38 coordinate `10:112998590-C-T` and save raw output to disk
- Run a PheWAS search for variant `10:114758349:C:T` with max 25 results

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From the same set: [openai/plugins](https://affpapa.org/en/nevibecode/by/openai/plugins.md) — 528 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