name: encode-skill
description: Submit compact ENCODE REST API requests for object lookups, portal-style search, and metadata retrieval. Use when a user wants concise ENCODE summaries
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.
By