Update to Life Sciences Databases

{
  "name": "efo-ontology-skill",
  "description": "Submit compact EFO OLS4 requests for search, term lookup, children, and descendants. Use when a user wants concise EFO resolution or ontology-expansion summaries",
  "included_files": [
    {
      "relative_path": "scripts/rest_request.py",
      "size_in_bytes": 1097
    }
  ],
  "skill_md_contents": "---\nname: efo-ontology-skill\ndescription: Submit compact EFO OLS4 requests for search, term lookup, children, and descendants. Use when a user wants concise EFO resolution or ontology-expansion summaries\n---\n\n## Source presentation\n<!-- source-presentation-contract:v2 -->\n- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.\n- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.\n- Use the `efo-ontology-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.\n\n## Operating rules\n- Use `scripts/rest_request.py` for all OLS4 and EFO API calls.\n- Use `base_url=https://www.ebi.ac.uk/ols4/api`.\n- Search, children, and descendant endpoints are better with `max_items=10`; single term lookups usually do not need `max_items`.\n- Use the smallest ontology expansion that answers the question.\n- Re-run requests in long conversations instead of relying on older tool output.\n- Treat displayed `...` in tool previews as UI truncation, not literal request content.\n\n## Execution behavior\n- Return concise markdown summaries from the script JSON by default.\n- Prefer these paths: `search`, `ontologies/efo/terms/<double-encoded-iri>`, and the corresponding `children` or `descendants` paths.\n- If the user needs the full payload, set `save_raw=true` and report the saved file path.\n\n## Input\n- Read one JSON object from stdin.\n- Required fields: `base_url`, `path`\n- Optional fields: `method`, `params`, `headers`, `json_body`, `form_body`, `record_path`, `response_format`, `max_items`, `max_depth`, `timeout_sec`, `save_raw`, `raw_output_path`\n- Common OLS4 patterns:\n  - `{\"base_url\":\"https://www.ebi.ac.uk/ols4/api\",\"path\":\"search\",\"params\":{\"q\":\"asthma\",\"ontology\":\"efo\"},\"record_path\":\"response.docs\",\"max_items\":10}`\n  - `{\"base_url\":\"https://www.ebi.ac.uk/ols4/api\",\"path\":\"ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0000270\"}`\n  - `{\"base_url\":\"https://www.ebi.ac.uk/ols4/api\",\"path\":\"ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0000270/descendants\",\"record_path\":\"_embedded.terms\",\"max_items\":10}`\n\n## Output\n- Success returns `ok`, `source`, `path`, `method`, `status_code`, `warnings`, and either compact `records` or a compact `summary`.\n- Use `raw_output_path` when `save_raw=true`.\n- Failure returns `ok=false` with `error.code` and `error.message`.\n\n## Execution\n```bash\necho '{\"base_url\":\"https://www.ebi.ac.uk/ols4/api\",\"path\":\"search\",\"params\":{\"q\":\"asthma\",\"ontology\":\"efo\"},\"record_path\":\"response.docs\",\"max_items\":10}' | python scripts/rest_request.py\n```\n"
}