Encode Skill

Operating rules

• Use scripts/rest_request.py for all ENCODE API calls.
• Use base_url=https://www.encodeproject.org.
• Object lookups usually do not need max_items; portal-style search endpoints are better with limit=10 and max_items=10.
• Send Accept: application/json in headers and add format=json in params when needed.
• Keep request volume modest and avoid large unfiltered searches.
• 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 accession paths such as biosamples/<accession>/ and search paths such as search/.
• 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 ENCODE patterns:
• {"base_url":"https://www.encodeproject.org","path":"biosamples/ENCBS000AAA/","params":{"frame":"object","format":"json"},"headers":{"Accept":"application/json"}}
• {"base_url":"https://www.encodeproject.org","path":"search/","params":{"type":"Experiment","assay_term_name":"RNA-seq","limit":10,"format":"json"},"record_path":"@graph","headers":{"Accept":"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://www.encodeproject.org","path":"search/","params":{"type":"Experiment","assay_term_name":"RNA-seq","limit":10,"format":"json"},"record_path":"@graph","headers":{"Accept":"application/json"},"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.