# ensembl-skill

Runs lightweight Ensembl REST API queries to deliver concise summaries of genes, genomic regions, and genetic variations.

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

## What it does

The skill talks to `https://rest.ensembl.org` through a bundled Python helper `scripts/rest_request.py`. Rather than flooding the context window with large JSON payloads, it converts biological records into short Markdown summaries. Raw JSON output is printed only when explicitly requested.

It focuses on standard Ensembl endpoints: identifier lookups (`lookup/id/<id>`), region overlaps (`overlap/region/<species>/<region>`), cross-references (`xrefs/id/<id>`), and variant records (`variation/<species>/<id>`). For region queries, the script limits output with `max_items=10` to avoid context bloat.

Because the helper reads input parameters as JSON from standard input, Python must be available in the local environment. When complete uncompressed responses are needed, setting `save_raw=true` alongside `raw_output_path` dumps the payload directly to a file.

## Install

### Codex (native platform)

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

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

### Claude Code

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

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

### Cursor

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

### GitHub Copilot

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

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

### Gemini CLI

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

### Windsurf (Devin Desktop)

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

## When to use it
- fetch gene details by Ensembl identifier
- inspect genomic features overlapping a chromosomal region
- retrieve cross-references for a biological entity
- query variant annotations across species

## Example prompts
- Look up gene ENSG00000141510 in Ensembl
- Find overlapping genes in region homo_sapiens 1:1000000-1002000
- Fetch cross-references for this Ensembl ID and summarize them

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From the same set: [openai/plugins](https://affpapa.org/en/nevibecode/by/openai/plugins.md) — 420 cards

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