Update to Life Sciences Databases

{
  "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": 8660
    },
    {
      "relative_path": "scripts/variant_resolution.py",
      "size_in_bytes": 362
    }
  ],
  "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## Source presentation\n<!-- source-presentation-contract:v2 -->\n- Add claim-adjacent links only for substantive claims supported by returned `sources`; never cite empty, metadata-only, or failed lookups.\n- Preserve `checked_sources`, use only supported `canonical_url` mappings, and leave requested raw or machine-readable output unchanged.\n- Use the `biobankjapan-phewas-skill` entry in `../../references/source-links.json` and follow `../../references/source-presentation.md`.\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"
}