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.
By