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encode-skill

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

Stars
1,305
Source
openai/plugins
Updated
2026-05-30
Slug
openai--plugins--encode-skill
View on GitHubRaw SKILL.md

// install — copy + paste into any project

mkdir -p .claude/skills && curl -fsSL https://raw.githubusercontent.com/openai/plugins/HEAD/plugins/life-science-research/skills/encode-skill/SKILL.md -o .claude/skills/encode-skill.md

Drops the SKILL.md into .claude/skills/encode-skill.md. Works with Claude Code, Cursor, and any agent that loads SKILL.md files from .claude/skills/.

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.