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efo-ontology-skill

Search EFO, a structured vocabulary, look up individual terms, and retrieve their immediate children or broader descendants through OLS4. Get concise summaries for term identification and hierarchy exploration, with full responses saved when needed.

OriginalShow the original 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

See how to install

Good for

  • Find EFO terms related to a search word
  • Look up details for a specific EFO term
  • Explore immediate children and broader descendants
  • Save a full API response for inspection

Files included (3)

  • SKILL.md2.4 KB
  • agents/openai.yaml107 B
  • scripts/rest_request.py10.5 KB

SKILL.md (original)

Review the instructions the agent will receive before you install.

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.

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