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
• Common UniProt patterns:
  • {"base_url":"https://rest.uniprot.org","path":"uniprotkb/search","params":{"query":"gene:TP53 AND organism_id:9606","fields":"accession,gene_names","size":10,"format":"json"},"record_path":"results","max_items":10}
  • {"base_url":"https://rest.uniprot.org","path":"uniprotkb/P04637","params":{"format":"json"}}
  • {"base_url":"https://rest.uniprot.org","path":"uniprotkb/stream","params":{"query":"organism_id:562","format":"fasta","size":2},"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://rest.uniprot.org","path":"uniprotkb/search","params":{"query":"gene:TP53 AND organism_id:9606","fields":"accession,gene_names","size":10,"format":"json"},"record_path":"results","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.