Biobankjapan Phewas Skill

Operating rules

• Use scripts/biobankjapan_phewas.py for all BioBank Japan PheWAS lookups.
• Accept exactly one of rsid, grch37, grch38, or variant; resolve to the canonical GRCh37 chr:pos-ref-alt query before calling BioBank Japan.
• The script accepts max_results; start with max_results=10 and only increase it if the first slice is insufficient.
• Re-run the lookup 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 needs the full association payload, set save_raw=true and report raw_output_path instead of pasting large arrays into chat.

Execution behavior

• Return concise markdown summaries from the script JSON by default.
• Return the JSON verbatim only if the user explicitly asks for machine-readable output.
• Surface the canonical queried variant, total association count, whether the results were truncated, and every entry in warnings.
• A multi-allelic rsID is probed against each alternate allele in turn; report which canonical variant the counts came from, since it may not be the first alternate Ensembl lists.
• Increase max_results gradually instead of asking for large association dumps in one call.

Input

• Read one JSON object from stdin, or a single JSON string containing the variant.
• Required input: exactly one of rsid, grch37, grch38, or variant
• Optional fields: max_results, save_raw, raw_output_path, timeout_sec
• Common patterns:
  • {"grch37":"10:114758349-C-T","max_results":10}
  • {"grch38":"10:112998590-C-T","max_results":10}
  • {"rsid":"rs7903146","max_results":10}
  • {"variant":"10:114758349:C:T","max_results":25,"save_raw":true}

Output

• Success returns ok, source, input, query_variant, max_results_applied, association_count, association_count_total, truncated, associations, variant, variant_url, raw_output_path, and warnings.
• Use raw_output_path when save_raw=true.
• Failure returns ok=false with error.code and error.message.

Execution

echo '{"grch37":"10:114758349-C-T","max_results":10}' | python scripts/biobankjapan_phewas.py

References

• No additional runtime references are required; keep the import package limited to this file and scripts/biobankjapan_phewas.py.