proteomexchange-skill

name	proteomexchange-skill
description	Submit compact ProteomeXchange PROXI requests for datasets, libraries, peptidoforms, proteins, PSMs, spectra, and USI examples. Use when a user wants concise PROXI summaries

Operating rules

• Use scripts/rest_request.py for all ProteomeXchange PROXI calls.
• Use base_url=https://proteomecentral.proteomexchange.org/api/proxi/v0.1.
• Collection endpoints are better with max_items=10; targeted identifier lookups usually do not need max_items.
• Keep requests narrow by identifier, spectrum, or dataset whenever possible.
• 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: datasets, datasets/<identifier>, libraries, peptidoforms, proteins, psms, spectra, and usi_examples.
• 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 PROXI patterns:
  • {"base_url":"https://proteomecentral.proteomexchange.org/api/proxi/v0.1","path":"datasets","max_items":10}
  • {"base_url":"https://proteomecentral.proteomexchange.org/api/proxi/v0.1","path":"datasets/PXD000001"}
  • {"base_url":"https://proteomecentral.proteomexchange.org/api/proxi/v0.1","path":"usi_examples","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://proteomecentral.proteomexchange.org/api/proxi/v0.1","path":"datasets","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.