uniprot-skill

Operating rules

• Use scripts/rest_request.py for all UniProt API calls.
• Use base_url=https://rest.uniprot.org.
• The script accepts max_items; for search endpoints, start with API size=10 and max_items=10.
• Single accession or cluster lookups usually do not need max_items.
• Re-run requests in long conversations instead of relying on older tool output.
• Treat displayed ... in tool previews as UI truncation, not part of the real request.
• If the user asks for full JSON or FASTA, set save_raw=true and report the saved file path instead of pasting the payload 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: uniprotkb/search, uniprotkb/<accession>, uniref/<cluster>, uniparc/search, and uniprotkb/stream.
• For stream, use response_format=text so the script returns only a short 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