efo-ontology-skill

---
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
---

## Operating rules
- Use `scripts/rest_request.py` for all OLS4 and EFO API calls.
- Use `base_url=https://www.ebi.ac.uk/ols4/api`.
- Search, children, and descendant endpoints are better with `max_items=10`; single term lookups usually do not need `max_items`.
- Use the smallest ontology expansion that answers the question.
- Re-run requests in long conversations instead of relying on older tool output.
- Treat displayed `...` in tool previews as UI truncation, not literal request content.

## Execution behavior
- Return concise markdown summaries from the script JSON by default.
- Prefer these paths: `search`, `ontologies/efo/terms/<double-encoded-iri>`, and the corresponding `children` or `descendants` paths.
- If the user needs the full payload, set `save_raw=true` and report the saved file path.

## 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 OLS4 patterns:
  - `{"base_url":"https://www.ebi.ac.uk/ols4/api","path":"search","params":{"q":"asthma","ontology":"efo"},"record_path":"response.docs","max_items":10}`
  - `{"base_url":"https://www.ebi.ac.uk/ols4/api","path":"ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0000270"}`
  - `{"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}`

## 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://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
```

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