# Ensembl Skill

> Submit compact Ensembl REST API requests for lookup, overlap, cross-reference, and variation endpoints. Use when a user wants concise Ensembl summaries

- Skill: `concertonotes/ensembl-skill` (Agent Skill, multi-file: 3 files)
- Install (CLI): `npx skillmds@latest add concertonotes/ensembl-skill`
- Raw SKILL.md: https://api.skillmd.com/api/skills/concertonotes/ensembl-skill/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Research & Search
- Author: ConcertoNotes (https://skillmd.com/u/concertonotes)
- Updated: 2026-09-08
- Page: https://skillmd.com/skills/concertonotes/ensembl-skill

---


## Operating rules
- Use `scripts/rest_request.py` for all Ensembl API calls.
- Use `base_url=https://rest.ensembl.org`.
- The script accepts `max_items`; object lookups usually do not need it, but `overlap` and `xrefs` are better with `max_items=10`.
- Send JSON-friendly headers such as `Accept: application/json` and `Content-Type: application/json`.
- Re-run requests in long conversations instead of relying on older tool output.
- Treat displayed `...` in tool previews as UI truncation, not part of the true request.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Return the script JSON verbatim only if the user explicitly asks for machine-readable output.
- Prefer these paths: `lookup/id/<id>`, `overlap/region/<species>/<region>`, `xrefs/id/<id>`, and `variation/<species>/<id>`.
- Use `save_raw=true` when the user needs the full payload.

## Input
- Read one JSON object from stdin.
- Required fields: `base_url`, `path`
- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`
- Common Ensembl patterns:
  - `{"base_url":"https://rest.ensembl.org","path":"lookup/id/ENSG00000141510","headers":{"Accept":"application/json","Content-Type":"application/json"}}`
  - `{"base_url":"https://rest.ensembl.org","path":"overlap/region/homo_sapiens/1:1000000-1002000","params":{"feature":"gene"},"headers":{"Accept":"application/json","Content-Type":"application/json"},"max_items":10}`

## Output
- Success returns `ok`, `source`, `path`, `method`, `status_code`, `warnings`, and either compact `records` or a compact `summary`.
- Use `raw_output_path` when `save_raw=true`.
- Failure returns `ok=false` with `error.code` and `error.message`.

## Execution
```bash
echo '{"base_url":"https://rest.ensembl.org","path":"lookup/id/ENSG00000141510","headers":{"Accept":"application/json","Content-Type":"application/json"}}' | python scripts/rest_request.py
```

## References
- No additional runtime references are required; keep the import package limited to this file and `scripts/rest_request.py`.