efo-ontology-skill

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

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

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.