{"id":24688,"plugin_id":"plugins~Plugin_7113e6f705948191bad2d24c30465361","kind":"skill","collection_source":null,"comparison_source":null,"observed_at":"2026-09-30T23:18:35.146Z","digest":"4b3de24e1cffe3b87e78aac7306fc52b82c94c8e22276e4d1c3bd687335a3cb3","against":null,"payload":{"name":"biobankjapan-phewas-skill","description":"Fetch compact BioBank Japan PheWAS summaries for single variants by accepting rsID, GRCh38, or GRCh37 input and resolving to the required GRCh37 query. Use when a user wants concise BBJ association results for one variant","included_files":[{"relative_path":"agents/openai.yaml","size_in_bytes":113},{"relative_path":"scripts/biobankjapan_phewas.py","size_in_bytes":7541},{"relative_path":"scripts/variant_resolution.py","size_in_bytes":12206}],"skill_md_contents":"---\nname: biobankjapan-phewas-skill\ndescription: Fetch compact BioBank Japan PheWAS summaries for single variants by accepting rsID, GRCh38, or GRCh37 input and resolving to the required GRCh37 query. Use when a user wants concise BBJ association results for one variant\n---\n\n## Operating rules\n- Use `scripts/biobankjapan_phewas.py` for all BioBank Japan PheWAS lookups.\n- Accept exactly one of `rsid`, `grch37`, `grch38`, or `variant`; resolve to the canonical GRCh37 `chr:pos-ref-alt` query before calling BioBank Japan.\n- The script accepts `max_results`; start with `max_results=10` and only increase it if the first slice is insufficient.\n- Re-run the lookup in long conversations instead of relying on older tool output.\n- Treat displayed `...` in tool previews as UI truncation, not literal request content.\n- If the user needs the full association payload, set `save_raw=true` and report `raw_output_path` instead of pasting large arrays into chat.\n\n## Execution behavior\n- Return concise markdown summaries from the script JSON by default.\n- Return the JSON verbatim only if the user explicitly asks for machine-readable output.\n- Surface the canonical queried variant, total association count, and whether the results were truncated.\n- Increase `max_results` gradually instead of asking for large association dumps in one call.\n\n## Input\n- Read one JSON object from stdin, or a single JSON string containing the variant.\n- Required input: exactly one of `rsid`, `grch37`, `grch38`, or `variant`\n- Optional fields: `max_results`, `save_raw`, `raw_output_path`, `timeout_sec`\n- Common patterns:\n  - `{\"grch37\":\"10:114758349-C-T\",\"max_results\":10}`\n  - `{\"grch38\":\"10:112998590-C-T\",\"max_results\":10}`\n  - `{\"rsid\":\"rs7903146\",\"max_results\":10}`\n  - `{\"variant\":\"10:114758349:C:T\",\"max_results\":25,\"save_raw\":true}`\n\n## Output\n- 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`.\n- Use `raw_output_path` when `save_raw=true`.\n- Failure returns `ok=false` with `error.code` and `error.message`.\n\n## Execution\n```bash\necho '{\"grch37\":\"10:114758349-C-T\",\"max_results\":10}' | python scripts/biobankjapan_phewas.py\n```\n\n## References\n- No additional runtime references are required; keep the import package limited to this file and `scripts/biobankjapan_phewas.py`.\n"},"changes":[],"summary":"First saved snapshot. No earlier version is available for comparison.","summary_kind":"deterministic","summary_metadata":{}}