ensembl-skill

Imported from openai/plugins (plugins/life-science-research/skills/ensembl-skill/SKILL.md). Install upstream with npx skills add openai/plugins --skill ensembl-skill. Copyright stays with the author.

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

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.