human-protein-atlas-skill

name: human-protein-atlas-skill description: Submit compact Human Protein Atlas requests for gene JSON, search downloads, and page-level tissue or cell-line lookups. Use when a user wants concise Human Protein Atlas summaries; save raw JSON or HTML only on request.

Operating rules

• Use scripts/rest_request.py for all Human Protein Atlas calls.
• Use base_url=https://www.proteinatlas.org.
• The script accepts max_items; single gene entry lookups usually do not need it, while search and download endpoints are better with max_items=10.
• 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.
• If the user asks for full HTML or JSON, set save_raw=true and report the saved file path instead of pasting large payloads into chat.

Execution behavior

• Return concise markdown summaries from the script JSON by default.
• Return the script JSON verbatim only if the user explicitly asks for machine-readable output.
• Prefer these paths: <ENSG>.json, api/search_download.php, search/tissue/<symbol>, and search/cellline/<symbol>.
• For page-level search endpoints, prefer response_format=text so the script returns only text_head unless raw output is requested.

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 HPA patterns:
  • {"base_url":"https://www.proteinatlas.org","path":"ENSG00000141510.json"}
  • {"base_url":"https://www.proteinatlas.org","path":"api/search_download.php","params":{"search":"TP53","format":"json","columns":"g,gs,tissue","compress":"no"},"max_items":10}
  • {"base_url":"https://www.proteinatlas.org","path":"search/tissue/TP53","response_format":"text"}

Output

• Success returns ok, source, path, method, status_code, warnings, and either compact records, a compact summary, or text_head.
• Use raw_output_path when save_raw=true.
• Failure returns ok=false with error.code and error.message.

Execution

echo '{"base_url":"https://www.proteinatlas.org","path":"ENSG00000141510.json"}' | 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.