@nahisaho/satori 0.25.5 → 0.27.0

package/bin/satori.js

@@ -1,7 +1,7 @@
 #!/usr/bin/env node
 
-const fs = require('fs');
-const path = require('path');
+const fs = require('node:fs');
+const path = require('node:path');
 
 const COMMAND = process.argv[2];
 const SUBCOMMAND = process.argv[3];
@@ -71,50 +71,410 @@ SATORI — Agent Skills for Science
 
 Usage:
   satori init [--force] [--dry-run]   Install .github/ skills into current directory
+  satori skill search <query>         Search skills by keyword
+  satori skill info <name>            Show detailed skill information
   satori pipeline suggest             Interactive pipeline recommendation
   satori pipeline list                List all available pipelines
+  satori validate [--verbose]         Validate all SKILL.md files
+  satori stats                        Show skill/TU coverage statistics
   satori help                         Show this help message
   satori --version, -v                Show version number
 
 Options:
   --force     Overwrite existing .github/ directory
   --dry-run   Preview what would be installed without making changes
+  --verbose   Show detailed validation output
 `);
 }
 
 // ── Pipeline Suggest ──
 
 const PIPELINES = [
-  { id: 1,  name: '仮説検証→論文化', domain: 'general',    keywords: ['仮説', '統計', '論文', 'hypothesis'], skills: 'hypothesis-engine → data-preprocessing → statistical-testing → ml-classification → publication-figures → academic-writing → critical-review' },
-  { id: 2,  name: 'バリアント→臨床', domain: 'genomics',   keywords: ['バリアント', 'variant', 'VCF', 'WGS', 'WES'], skills: 'variant-interpretation → pharmacogenomics → precision-oncology → clinical-decision-support → clinical-reporting' },
-  { id: 3,  name: 'トランスクリプトーム', domain: 'genomics', keywords: ['RNA-seq', 'トランスクリプトーム', 'DEG', '発現'], skills: 'rnaseq-analysis → pathway-enrichment → network-analysis → publication-figures' },
-  { id: 4,  name: 'エピジェネティクス', domain: 'genomics', keywords: ['エピゲノム', 'ChIP-seq', 'ATAC-seq', 'メチル化'], skills: 'epigenomics-chromatin → regulatory-genomics → noncoding-rna → gene-regulation' },
-  { id: 5,  name: 'AlphaFold 構造解析', domain: 'structural', keywords: ['AlphaFold', 'タンパク質構造', '3D', 'protein structure'], skills: 'alphafold-structures → protein-structure-analysis → molecular-docking' },
-  { id: 6,  name: 'エビデンス合成', domain: 'literature', keywords: ['メタアナリシス', 'systematic review', '文献', 'エビデンス'], skills: 'deep-research → literature-search → meta-analysis → evidence-synthesis → academic-writing → critical-review' },
-  { id: 7,  name: '創薬パイプライン', domain: 'pharma',    keywords: ['創薬', 'drug discovery', 'ADMET', 'ドッキング'], skills: 'drug-target-profiling → compound-screening → molecular-docking → admet-pharmacokinetics → drug-repurposing' },
-  { id: 8,  name: 'ML/XAI パイプライン', domain: 'ml',     keywords: ['機械学習', 'ML', 'SHAP', 'XAI', '予測モデル'], skills: 'data-preprocessing → ml-classification → ml-regression → explainable-ai → fairness-bias → publication-figures' },
-  { id: 9,  name: '環境・生態学', domain: 'ecology',       keywords: ['生態', '生物多様性', 'SDM', '環境', 'ecology'], skills: 'environmental-ecology → biodiversity-conservation → species-distribution → time-series-forecasting' },
-  { id: 10, name: '計算材料科学', domain: 'materials',     keywords: ['材料', 'materials', 'DFT', '物性'], skills: 'computational-materials → cheminformatics → molecular-dynamics → ml-regression' },
-  { id: 11, name: '医薬品安全性', domain: 'pharma',        keywords: ['有害事象', 'ファーマコビジランス', '安全性', 'adverse'], skills: 'pharmacovigilance → pharmacogenomics → regulatory-science' },
-  { id: 12, name: '希少疾患', domain: 'clinical',          keywords: ['希少疾患', 'rare disease', 'Orphanet'], skills: 'rare-disease-genetics → gene-panel-design → variant-interpretation → clinical-reporting' },
-  { id: 13, name: 'がんゲノミクス', domain: 'oncology',    keywords: ['がん', 'cancer', 'TMB', '体細胞変異'], skills: 'cancer-genomics → precision-oncology → biomarker-discovery → clinical-reporting' },
-  { id: 14, name: 'GWAS・集団遺伝学', domain: 'genomics', keywords: ['GWAS', '集団遺伝学', 'population genetics', 'biobank'], skills: 'biobank-cohort → population-genetics → statistical-testing → publication-figures' },
-  { id: 15, name: 'シングルセル', domain: 'genomics',      keywords: ['シングルセル', 'single-cell', 'scRNA-seq', '空間トランスクリプトーム'], skills: 'cellxgene-census → scvi-integration → spatial-transcriptomics → gene-regulation' },
-  { id: 16, name: 'プロテオミクス', domain: 'omics',       keywords: ['プロテオミクス', 'proteomics', '質量分析'], skills: 'proteomics → protein-structure-analysis → network-analysis' },
-  { id: 17, name: 'メタボロミクス', domain: 'omics',       keywords: ['メタボロミクス', 'metabolomics', '代謝物', '脂質'], skills: 'metabolomics → lipidomics → systems-biology → network-analysis' },
-  { id: 18, name: 'マイクロバイオーム', domain: 'ecology', keywords: ['マイクロバイオーム', 'metagenome', '16S', '腸内細菌'], skills: 'microbiome-metagenomics → metagenome-assembled-genomes → phylogenetics → environmental-ecology' },
-  { id: 19, name: 'パスウェイ・KG', domain: 'systems',     keywords: ['パスウェイ', 'ナレッジグラフ', 'knowledge graph', 'pathway'], skills: 'gene-id-mapping → pathway-enrichment → ontology-integration → network-analysis → knowledge-graph' },
-  { id: 20, name: '農業・食品', domain: 'agriculture',     keywords: ['農業', '食品', 'agriculture', 'food safety'], skills: 'agricultural-science → food-science-nutrition → environmental-ecology' },
-  { id: 21, name: '臨床情報学', domain: 'clinical',        keywords: ['臨床', 'EHR', 'FHIR', 'OMOP', '電子カルテ'], skills: 'clinical-standards → clinical-nlp → clinical-reporting → healthcare-ai → survival-clinical' },
-  { id: 22, name: 'ロボティクス・IoT', domain: 'engineering', keywords: ['ロボティクス', 'IoT', 'ロボット', 'robotics'], skills: 'robotics-automation → lab-automation → lab-data-management → interactive-dashboard' },
-  { id: 23, name: '実験計画・統計', domain: 'general',     keywords: ['実験計画', 'DOE', '検出力', 'サンプルサイズ'], skills: 'experimental-design → statistical-testing → reproducibility-assessment → publication-figures' },
-  { id: 24, name: '科学的可視化', domain: 'general',       keywords: ['可視化', 'visualization', 'ダッシュボード', 'dashboard'], skills: 'publication-figures → interactive-dashboard' },
-  { id: 25, name: '学術出版', domain: 'literature',        keywords: ['論文投稿', 'journal', 'グラント', 'grant'], skills: 'academic-writing → critical-review → citation-network' },
-  { id: 26, name: '科学教育', domain: 'education',         keywords: ['教育', 'education', 'カリキュラム'], skills: 'science-education → reproducibility-assessment' },
+  {
+    id: 1,
+    name: '仮説検証→論文化',
+    domain: 'general',
+    keywords: ['仮説', '統計', '論文', 'hypothesis'],
+    skills:
+      'hypothesis-engine → data-preprocessing → statistical-testing → ml-classification → publication-figures → academic-writing → critical-review',
+  },
+  {
+    id: 2,
+    name: 'バリアント→臨床',
+    domain: 'genomics',
+    keywords: ['バリアント', 'variant', 'VCF', 'WGS', 'WES'],
+    skills:
+      'variant-interpretation → pharmacogenomics → precision-oncology → clinical-decision-support → clinical-reporting',
+  },
+  {
+    id: 3,
+    name: 'トランスクリプトーム',
+    domain: 'genomics',
+    keywords: ['RNA-seq', 'トランスクリプトーム', 'DEG', '発現'],
+    skills: 'rnaseq-analysis → pathway-enrichment → network-analysis → publication-figures',
+  },
+  {
+    id: 4,
+    name: 'エピジェネティクス',
+    domain: 'genomics',
+    keywords: ['エピゲノム', 'ChIP-seq', 'ATAC-seq', 'メチル化'],
+    skills: 'epigenomics-chromatin → regulatory-genomics → noncoding-rna → gene-regulation',
+  },
+  {
+    id: 5,
+    name: 'AlphaFold 構造解析',
+    domain: 'structural',
+    keywords: ['AlphaFold', 'タンパク質構造', '3D', 'protein structure'],
+    skills: 'alphafold-structures → protein-structure-analysis → molecular-docking',
+  },
+  {
+    id: 6,
+    name: 'エビデンス合成',
+    domain: 'literature',
+    keywords: ['メタアナリシス', 'systematic review', '文献', 'エビデンス'],
+    skills:
+      'deep-research → literature-search → meta-analysis → evidence-synthesis → academic-writing → critical-review',
+  },
+  {
+    id: 7,
+    name: '創薬パイプライン',
+    domain: 'pharma',
+    keywords: ['創薬', 'drug discovery', 'ADMET', 'ドッキング'],
+    skills:
+      'drug-target-profiling → compound-screening → molecular-docking → admet-pharmacokinetics → drug-repurposing',
+  },
+  {
+    id: 8,
+    name: 'ML/XAI パイプライン',
+    domain: 'ml',
+    keywords: ['機械学習', 'ML', 'SHAP', 'XAI', '予測モデル'],
+    skills:
+      'data-preprocessing → ml-classification → ml-regression → explainable-ai → fairness-bias → publication-figures',
+  },
+  {
+    id: 9,
+    name: '環境・生態学',
+    domain: 'ecology',
+    keywords: ['生態', '生物多様性', 'SDM', '環境', 'ecology'],
+    skills: 'environmental-ecology → biodiversity-conservation → species-distribution → time-series-forecasting',
+  },
+  {
+    id: 10,
+    name: '計算材料科学',
+    domain: 'materials',
+    keywords: ['材料', 'materials', 'DFT', '物性'],
+    skills: 'computational-materials → cheminformatics → molecular-dynamics → ml-regression',
+  },
+  {
+    id: 11,
+    name: '医薬品安全性',
+    domain: 'pharma',
+    keywords: ['有害事象', 'ファーマコビジランス', '安全性', 'adverse'],
+    skills: 'pharmacovigilance → pharmacogenomics → regulatory-science',
+  },
+  {
+    id: 12,
+    name: '希少疾患',
+    domain: 'clinical',
+    keywords: ['希少疾患', 'rare disease', 'Orphanet'],
+    skills: 'rare-disease-genetics → gene-panel-design → variant-interpretation → clinical-reporting',
+  },
+  {
+    id: 13,
+    name: 'がんゲノミクス',
+    domain: 'oncology',
+    keywords: ['がん', 'cancer', 'TMB', '体細胞変異'],
+    skills: 'cancer-genomics → precision-oncology → biomarker-discovery → clinical-reporting',
+  },
+  {
+    id: 14,
+    name: 'GWAS・集団遺伝学',
+    domain: 'genomics',
+    keywords: ['GWAS', '集団遺伝学', 'population genetics', 'biobank'],
+    skills: 'biobank-cohort → population-genetics → statistical-testing → publication-figures',
+  },
+  {
+    id: 15,
+    name: 'シングルセル',
+    domain: 'genomics',
+    keywords: ['シングルセル', 'single-cell', 'scRNA-seq', '空間トランスクリプトーム'],
+    skills: 'cellxgene-census → scvi-integration → spatial-transcriptomics → gene-regulation',
+  },
+  {
+    id: 16,
+    name: 'プロテオミクス',
+    domain: 'omics',
+    keywords: ['プロテオミクス', 'proteomics', '質量分析'],
+    skills: 'proteomics → protein-structure-analysis → network-analysis',
+  },
+  {
+    id: 17,
+    name: 'メタボロミクス',
+    domain: 'omics',
+    keywords: ['メタボロミクス', 'metabolomics', '代謝物', '脂質'],
+    skills: 'metabolomics → lipidomics → systems-biology → network-analysis',
+  },
+  {
+    id: 18,
+    name: 'マイクロバイオーム',
+    domain: 'ecology',
+    keywords: ['マイクロバイオーム', 'metagenome', '16S', '腸内細菌'],
+    skills: 'microbiome-metagenomics → metagenome-assembled-genomes → phylogenetics → environmental-ecology',
+  },
+  {
+    id: 19,
+    name: 'パスウェイ・KG',
+    domain: 'systems',
+    keywords: ['パスウェイ', 'ナレッジグラフ', 'knowledge graph', 'pathway'],
+    skills: 'gene-id-mapping → pathway-enrichment → ontology-integration → network-analysis → knowledge-graph',
+  },
+  {
+    id: 20,
+    name: '農業・食品',
+    domain: 'agriculture',
+    keywords: ['農業', '食品', 'agriculture', 'food safety'],
+    skills: 'agricultural-science → food-science-nutrition → environmental-ecology',
+  },
+  {
+    id: 21,
+    name: '臨床情報学',
+    domain: 'clinical',
+    keywords: ['臨床', 'EHR', 'FHIR', 'OMOP', '電子カルテ'],
+    skills: 'clinical-standards → clinical-nlp → clinical-reporting → healthcare-ai → survival-clinical',
+  },
+  {
+    id: 22,
+    name: 'ロボティクス・IoT',
+    domain: 'engineering',
+    keywords: ['ロボティクス', 'IoT', 'ロボット', 'robotics'],
+    skills: 'robotics-automation → lab-automation → lab-data-management → interactive-dashboard',
+  },
+  {
+    id: 23,
+    name: '実験計画・統計',
+    domain: 'general',
+    keywords: ['実験計画', 'DOE', '検出力', 'サンプルサイズ'],
+    skills: 'experimental-design → statistical-testing → reproducibility-assessment → publication-figures',
+  },
+  {
+    id: 24,
+    name: '科学的可視化',
+    domain: 'general',
+    keywords: ['可視化', 'visualization', 'ダッシュボード', 'dashboard'],
+    skills: 'publication-figures → interactive-dashboard',
+  },
+  {
+    id: 25,
+    name: '学術出版',
+    domain: 'literature',
+    keywords: ['論文投稿', 'journal', 'グラント', 'grant'],
+    skills: 'academic-writing → critical-review → citation-network',
+  },
+  {
+    id: 26,
+    name: '科学教育',
+    domain: 'education',
+    keywords: ['教育', 'education', 'カリキュラム'],
+    skills: 'science-education → reproducibility-assessment',
+  },
+  // ── クロスドメインパイプライン ──
+  {
+    id: 'A',
+    name: 'ゲノム創薬統合',
+    domain: 'cross-domain',
+    keywords: ['ゲノム創薬', 'GWAS', '創薬ターゲット', 'drug target', 'biobank'],
+    skills:
+      'biobank-cohort → population-genetics → drug-target-profiling → compound-screening → molecular-docking → admet-pharmacokinetics',
+  },
+  {
+    id: 'B',
+    name: 'AI 駆動臨床意思決定',
+    domain: 'cross-domain',
+    keywords: ['臨床AI', '予後予測', 'SHAP', '患者', 'clinical AI'],
+    skills: 'clinical-decision-support → healthcare-ai → explainable-ai → pharmacovigilance → regulatory-science',
+  },
+  {
+    id: 'C',
+    name: '研究自動化',
+    domain: 'cross-domain',
+    keywords: ['研究自動化', '論文化', '仮説', 'research automation'],
+    skills:
+      'deep-research → hypothesis-pipeline → pipeline-scaffold → data-preprocessing → statistical-testing → publication-figures → academic-writing → systematic-review',
+  },
+  {
+    id: 'D',
+    name: 'マルチオミクス疾患解明',
+    domain: 'cross-domain',
+    keywords: ['マルチオミクス', '疾患', 'scRNA-seq', 'GRN', 'multi-omics'],
+    skills:
+      'single-cell-genomics → spatial-transcriptomics → disease-research → systems-biology → multi-omics → network-analysis',
+  },
+  {
+    id: 'E',
+    name: '個別化薬物療法',
+    domain: 'cross-domain',
+    keywords: ['個別化医療', 'PGx', 'Star アレル', '投与量最適化', 'pharmacogenomics'],
+    skills:
+      'variant-interpretation → pharmacogenomics → drug-target-profiling → admet-pharmacokinetics → clinical-decision-support → pharmacovigilance',
+  },
+  {
+    id: 'F',
+    name: 'バイオインフォマティクス完全',
+    domain: 'cross-domain',
+    keywords: ['バイオインフォマティクス', 'FASTQ', '配列解析', '統合パイプライン'],
+    skills:
+      'bioinformatics → single-cell-genomics → biobank-cohort → multi-omics → population-genetics → systems-biology → hypothesis-pipeline → academic-writing',
+  },
+  {
+    id: 'G',
+    name: 'がん精密医療 End-to-End',
+    domain: 'cross-domain',
+    keywords: ['がん精密医療', 'GDC', 'DepMap', '精密腫瘍学', 'TCGA'],
+    skills:
+      'gdc-portal → cancer-genomics → depmap-dependencies → civic-evidence → pharos-targets → compound-screening → precision-oncology → clinical-decision-support → healthcare-ai → survival-clinical',
+  },
+  {
+    id: 'H',
+    name: 'マルチオミクス縦断統合',
+    domain: 'cross-domain',
+    keywords: ['縦断統合', 'エピゲノム', 'プロテオーム', 'パスウェイ', 'VEP'],
+    skills:
+      'genome-sequence-tools → bioinformatics → variant-effect-prediction → epigenomics-chromatin → regulatory-genomics → cellxgene-census → scvi-integration → uniprot-proteome → alphafold-structures → protein-interaction-network → pathway-enrichment → reactome-pathways → network-visualization',
+  },
+  {
+    id: 'I',
+    name: '環境メタボ・マイクロバイオーム One Health',
+    domain: 'cross-domain',
+    keywords: ['One Health', '環境メタボ', '土壌', '微生物群集', 'SDM'],
+    skills:
+      'environmental-ecology → environmental-geodata → geospatial-analysis → microbiome-metagenomics → metagenome-assembled-genomes → phylogenetics → metabolomics-databases → metabolomics-network → metabolic-modeling → toxicology-env → publication-figures',
+  },
+  {
+    id: 'J',
+    name: 'AI 駆動マテリアルズインフォマティクス',
+    domain: 'cross-domain',
+    keywords: ['マテリアルズインフォマティクス', 'GNN', '能動学習', 'Materials Project', '材料探索'],
+    skills:
+      'computational-materials → cheminformatics → automl → graph-neural-networks → uncertainty-quantification → active-learning → doe → bayesian-statistics → adaptive-experiments → materials-characterization → advanced-visualization',
+  },
+  {
+    id: 'K',
+    name: '研究ライフサイクル完全自動化',
+    domain: 'cross-domain',
+    keywords: ['研究ライフサイクル', 'ラボ自動化', 'LIMS', 'ダッシュボード', 'グラント'],
+    skills:
+      'lab-automation → lab-data-management → streaming-analytics → model-monitoring → data-profiling → advanced-visualization → interactive-dashboard → scientific-schematics → reproducible-reporting → paper-quality → latex-formatter → peer-review-response → grant-writing → preprint-archive',
+  },
+  {
+    id: 'L',
+    name: 'AI 駆動エビデンス合成',
+    domain: 'cross-domain',
+    keywords: ['エビデンス合成AI', 'DL文献', 'AutoML', 'スクリーニング'],
+    skills:
+      'deep-research → literature-search → text-mining-nlp → deep-learning → transfer-learning → automl → meta-analysis → explainable-ai → systematic-review → academic-writing',
+  },
+  {
+    id: 'M',
+    name: 'がんマルチレイヤーゲノム創薬',
+    domain: 'cross-domain',
+    keywords: ['がんゲノム創薬', 'ICGC', 'ChEMBL', 'エピゲノム'],
+    skills:
+      'gdc-portal → cancer-genomics → icgc-cancer-data → ensembl-genomics → variant-effect-prediction → epigenomics-chromatin → gwas-catalog → pharos-targets → chembl-assay-mining → compound-screening',
+  },
+  {
+    id: 'N',
+    name: '臨床→規制→出版バリューチェーン',
+    domain: 'cross-domain',
+    keywords: ['バリューチェーン', 'EHR', '規制報告', '学術出版', 'HL7'],
+    skills:
+      'clinical-standards → clinical-nlp → clinical-reporting → healthcare-ai → pharmacovigilance → regulatory-science → reproducible-reporting → paper-quality → latex-formatter → peer-review-response',
+  },
+  {
+    id: 'O',
+    name: 'シングルセルプロテオーム統合',
+    domain: 'cross-domain',
+    keywords: ['シングルセルプロテオーム', '質量分析', '代謝モデル', 'MOFA+'],
+    skills:
+      'single-cell-genomics → spatial-transcriptomics → proteomics-mass-spectrometry → structural-proteomics → alphafold-structures → metabolomics-databases → metabolic-modeling → systems-biology → multi-omics',
+  },
+  // ── インダストリーパイプライン ──
+  {
+    id: 'Ind-1',
+    name: '製薬企業レギュラトリー',
+    domain: 'industry',
+    keywords: ['製薬', 'CTD', 'レギュラトリー', '規制申請', 'regulatory'],
+    skills:
+      'drug-target-profiling → molecular-docking → admet-pharmacokinetics → clinical-trials-analytics → pharmacovigilance → regulatory-science → reproducible-reporting → paper-quality',
+  },
+  {
+    id: 'Ind-2',
+    name: '農業バイオテクノロジー',
+    domain: 'industry',
+    keywords: ['農業バイオ', '土壌微生物', 'CRISPR', '圃場', 'ゲノム編集'],
+    skills:
+      'environmental-ecology → microbiome-metagenomics → geospatial-analysis → plant-biology → crispr-design → gene-expression-transcriptomics → doe → publication-figures',
+  },
+  {
+    id: 'Ind-3',
+    name: '臨床検査室ワークフロー',
+    domain: 'industry',
+    keywords: ['臨床検査', 'NGS', 'ACMG', 'PGx', '臨床レポート'],
+    skills:
+      'genome-sequence-tools → variant-interpretation → pharmacogenomics → clinical-decision-support → clinical-standards → clinical-nlp → clinical-reporting',
+  },
+  {
+    id: 'Ind-4',
+    name: '食品安全・毒性評価',
+    domain: 'industry',
+    keywords: ['食品安全', '毒性', '残留農薬', 'フードセーフティ', 'food safety'],
+    skills:
+      'microbiome-metagenomics → rrna-taxonomy → metabolomics-databases → metabolomics-network → toxicology-env → data-profiling → regulatory-science → publication-figures',
+  },
+  {
+    id: 'Ind-5',
+    name: '法医・公衆衛生',
+    domain: 'industry',
+    keywords: ['法医学', '公衆衛生', 'アウトブレイク', 'サーベイランス', 'forensic'],
+    skills:
+      'variant-interpretation → population-genetics → infectious-disease → phylogenetics → immunoinformatics → epidemiology-public-health → public-health-data → biobank-cohort',
+  },
+  // ── メソドロジーパイプライン ──
+  {
+    id: 'M-α',
+    name: 'ベイズ推論ワークフロー',
+    domain: 'methodology',
+    keywords: ['ベイズ', 'MCMC', '事後分布', 'Bayesian', '事前分布'],
+    skills:
+      'data-preprocessing → bayesian-statistics → statistical-simulation → uncertainty-quantification → doe → adaptive-experiments',
+  },
+  {
+    id: 'M-β',
+    name: '因果推論パイプライン',
+    domain: 'methodology',
+    keywords: ['因果推論', 'DAG', '傾向スコア', 'CATE', 'causal'],
+    skills:
+      'data-preprocessing → missing-data-analysis → causal-inference → causal-ml → explainable-ai → statistical-testing → publication-figures',
+  },
+  {
+    id: 'M-γ',
+    name: '時系列予測パイプライン',
+    domain: 'methodology',
+    keywords: ['時系列', 'Prophet', 'ARIMA', 'LSTM', '異常検知', 'forecasting'],
+    skills:
+      'data-preprocessing → time-series → time-series-forecasting → anomaly-detection → streaming-analytics → model-monitoring',
+  },
+  {
+    id: 'M-δ',
+    name: 'テキストマイニング・NLP',
+    domain: 'methodology',
+    keywords: ['テキストマイニング', 'NLP', 'PubTator', '引用ネットワーク', 'NER'],
+    skills:
+      'deep-research → literature-search → text-mining-nlp → biomedical-pubtator → clinical-nlp → semantic-scholar → citation-checker',
+  },
 ];
 
 function pipelineSuggest() {
-  const readline = require('readline');
+  const readline = require('node:readline');
   const rl = readline.createInterface({ input: process.stdin, output: process.stdout });
 
   const ask = (q) => new Promise((resolve) => rl.question(q, resolve));
@@ -162,6 +522,7 @@ function pipelineSuggest() {
         console.log(`  ... 他 ${scored.length - 5} 件`);
       }
       console.log('詳細は docs/SATORI_PIPELINE_EXAMPLES.md を参照してください。');
+      console.log('全パイプライン一覧は `satori pipeline list` で確認できます。');
     }
 
     rl.close();
@@ -169,14 +530,42 @@ function pipelineSuggest() {
 }
 
 function pipelineList() {
-  console.log('\n📋 SATORI パイプライン一覧 (26 ドメインパイプライン)\n');
-  for (const p of PIPELINES) {
+  const domain = PIPELINES.filter((p) => typeof p.id === 'number');
+  const cross = PIPELINES.filter((p) => p.domain === 'cross-domain');
+  const industry = PIPELINES.filter((p) => p.domain === 'industry');
+  const methodology = PIPELINES.filter((p) => p.domain === 'methodology');
+
+  console.log(`\n📋 SATORI パイプライン一覧 (全 ${PIPELINES.length} パイプライン)\n`);
+
+  console.log('── ドメインパイプライン (26) ──\n');
+  for (const p of domain) {
     console.log(`  #${String(p.id).padStart(2, ' ')}  ${p.name}`);
     console.log(`       ${p.skills}`);
     console.log('');
   }
-  console.log('クロスドメイン (15), 産業特化 (5), 方法論特化 (4) パイプラインは');
-  console.log('docs/SATORI_PIPELINE_EXAMPLES.md を参照してください。');
+
+  console.log('── クロスドメインパイプライン (15) ──\n');
+  for (const p of cross) {
+    console.log(`  #${p.id}   ${p.name}`);
+    console.log(`       ${p.skills}`);
+    console.log('');
+  }
+
+  console.log('── インダストリーパイプライン (5) ──\n');
+  for (const p of industry) {
+    console.log(`  #${p.id}  ${p.name}`);
+    console.log(`       ${p.skills}`);
+    console.log('');
+  }
+
+  console.log('── メソドロジーパイプライン (4) ──\n');
+  for (const p of methodology) {
+    console.log(`  #${p.id}  ${p.name}`);
+    console.log(`       ${p.skills}`);
+    console.log('');
+  }
+
+  console.log('詳細は docs/SATORI_PIPELINE_EXAMPLES.md を参照してください。');
 }
 
 function showVersion() {
@@ -184,10 +573,343 @@ function showVersion() {
   console.log(pkg.version);
 }
 
+// ── Validate ──
+
+function parseFrontmatter(content) {
+  const match = content.match(/^---\n([\s\S]*?)\n---/);
+  if (!match) return null;
+  const yaml = match[1];
+  const name = yaml.match(/^name:\s*(.+)$/m)?.[1]?.trim();
+  const hasDescription = /^description:/m.test(yaml);
+  return { name, hasDescription };
+}
+
+function validate() {
+  const verbose = FLAGS.includes('--verbose');
+  const skillsDir = path.join(SOURCE_DIR, 'skills');
+
+  if (!fs.existsSync(skillsDir)) {
+    console.error('Error: skills directory not found:', skillsDir);
+    process.exit(1);
+  }
+
+  const dirs = fs
+    .readdirSync(skillsDir)
+    .filter((d) => d.startsWith('scientific-'))
+    .sort();
+  let pass = 0;
+  let fail = 0;
+  const errors = [];
+
+  for (const dir of dirs) {
+    const filePath = path.join(skillsDir, dir, 'SKILL.md');
+    const issues = [];
+
+    if (!fs.existsSync(filePath)) {
+      issues.push('SKILL.md が見つかりません');
+    } else {
+      const content = fs.readFileSync(filePath, 'utf-8');
+      const fm = parseFrontmatter(content);
+
+      if (!fm) issues.push('YAML Frontmatter がありません');
+      else {
+        if (!fm.name) issues.push('Frontmatter に name がありません');
+        else if (fm.name !== dir) issues.push(`name 不一致: "${fm.name}" (期待値: "${dir}")`);
+        if (!fm.hasDescription) issues.push('Frontmatter に description がありません');
+      }
+
+      if (!/^# .+$/m.test(content)) issues.push('H1 タイトルがありません');
+      if (!/^## When to Use/m.test(content)) issues.push('## When to Use セクションがありません');
+      if (!/^## Quick Start/m.test(content)) issues.push('## Quick Start セクションがありません');
+      if (!/```(?:python|markdown|json)/.test(content)) issues.push('コードブロックがありません');
+    }
+
+    if (issues.length === 0) {
+      pass++;
+      if (verbose) console.log(`  ✔ ${dir}`);
+    } else {
+      fail++;
+      errors.push({ dir, issues });
+      if (verbose) {
+        console.log(`  ✘ ${dir}`);
+        for (const issue of issues) console.log(`      - ${issue}`);
+      }
+    }
+  }
+
+  console.log(`\n📋 SKILL.md 検証結果: ${pass} pass / ${fail} fail (全 ${dirs.length} スキル)`);
+
+  if (errors.length > 0 && !verbose) {
+    console.log('\n問題のあるスキル:');
+    for (const e of errors) {
+      console.log(`  ✘ ${e.dir}: ${e.issues.join(', ')}`);
+    }
+  }
+
+  if (fail > 0) {
+    console.log('\n詳細は --verbose オプションで確認してください。');
+    process.exit(1);
+  } else {
+    console.log('\n✔ 全スキルの検証に成功しました。');
+  }
+}
+
+// ── Stats ──
+
+function stats() {
+  const skillsDir = path.join(SOURCE_DIR, 'skills');
+
+  if (!fs.existsSync(skillsDir)) {
+    console.error('Error: skills directory not found:', skillsDir);
+    process.exit(1);
+  }
+
+  const dirs = fs
+    .readdirSync(skillsDir)
+    .filter((d) => d.startsWith('scientific-'))
+    .sort();
+  const totalSkills = dirs.length;
+  let tuLinked = 0;
+  let totalCodeBlocks = 0;
+  const tuPattern = /ToolUniverse|利用可能ツール|SMCP/i;
+  const tuKeyPattern = /`([A-Z][a-zA-Z]*_[a-z]+_[a-z_]+)`/g;
+  const allTuKeys = new Set();
+
+  for (const dir of dirs) {
+    const filePath = path.join(skillsDir, dir, 'SKILL.md');
+    if (!fs.existsSync(filePath)) continue;
+    const content = fs.readFileSync(filePath, 'utf-8');
+
+    if (tuPattern.test(content)) tuLinked++;
+
+    const codeBlocks = content.match(/```(?:python|markdown|json)/g);
+    if (codeBlocks) totalCodeBlocks += codeBlocks.length;
+
+    for (const m of content.matchAll(tuKeyPattern)) {
+      allTuKeys.add(m[1]);
+    }
+  }
+
+  const coverage = ((tuLinked / totalSkills) * 100).toFixed(1);
+  const pkg = require(path.join(PACKAGE_ROOT, 'package.json'));
+
+  console.log(`
+📊 SATORI v${pkg.version} — 統計
+
+  スキル総数:          ${totalSkills}
+  パイプライン数:      ${PIPELINES.length}
+  TU 連携スキル:       ${tuLinked} (${coverage}%)
+  TU 未連携:           ${totalSkills - tuLinked}
+  ユニーク TU キー:    ${allTuKeys.size}
+  コードブロック総数:  ${totalCodeBlocks}
+`);
+}
+
+// ── Skill Search / Info ──
+
+function loadAllSkills() {
+  const skillsDir = path.join(SOURCE_DIR, 'skills');
+  if (!fs.existsSync(skillsDir)) {
+    console.error('Error: skills directory not found:', skillsDir);
+    process.exit(1);
+  }
+  const dirs = fs
+    .readdirSync(skillsDir)
+    .filter((d) => d.startsWith('scientific-'))
+    .sort();
+  const skills = [];
+  for (const dir of dirs) {
+    const filePath = path.join(skillsDir, dir, 'SKILL.md');
+    if (!fs.existsSync(filePath)) continue;
+    const content = fs.readFileSync(filePath, 'utf-8');
+    const fm = parseFrontmatter(content);
+    const descMatch = content.match(/^description:\s*\|?\s*\n([\s\S]*?)(?=\n\w|\n---)/m);
+    const description = descMatch ? descMatch[1].replace(/^\s+/gm, '').trim() : fm?.hasDescription ? '' : '';
+    const tuKeyPattern = /`([A-Z][a-zA-Z]*_[a-z]+_[a-z_]+)`/g;
+    const tuKeys = [];
+    for (const m of content.matchAll(tuKeyPattern)) {
+      tuKeys.push(m[1]);
+    }
+    const h1Match = content.match(/^# (.+)$/m);
+    const title = h1Match ? h1Match[1].trim() : dir;
+    skills.push({ dir, name: fm?.name || dir, title, description, content, tuKeys });
+  }
+  return skills;
+}
+
+function skillSearch() {
+  const query = process.argv.slice(4).join(' ').toLowerCase();
+  if (!query) {
+    console.error('Error: 検索クエリを指定してください。');
+    console.log('Usage: satori skill search <query>');
+    process.exit(1);
+  }
+
+  const skills = loadAllSkills();
+  const scored = skills
+    .map((s) => {
+      let score = 0;
+      // 名前の完全一致
+      if (s.name.toLowerCase() === query) score += 10;
+      // 名前に含まれる
+      else if (s.name.toLowerCase().includes(query)) score += 5;
+      // タイトルに含まれる
+      if (s.title.toLowerCase().includes(query)) score += 3;
+      // 説明に含まれる
+      if (s.description.toLowerCase().includes(query)) score += 2;
+      // TU キーに含まれる
+      for (const k of s.tuKeys) {
+        if (k.toLowerCase().includes(query)) score += 1;
+      }
+      return { ...s, score };
+    })
+    .filter((s) => s.score > 0)
+    .sort((a, b) => b.score - a.score);
+
+  console.log(`\n🔍 "${process.argv.slice(4).join(' ')}" の検索結果\n`);
+  if (scored.length === 0) {
+    console.log('❌ 該当するスキルが見つかりませんでした。');
+    console.log('');
+    console.log('ヒント: 英語名（例: deep-learning, cancer-genomics）や');
+    console.log('       日本語キーワード（例: 創薬, 機械学習）で検索してみてください。');
+  } else {
+    const top = scored.slice(0, 10);
+    for (const s of top) {
+      const desc = s.description ? s.description.split('\n')[0].substring(0, 60) : '';
+      console.log(`  📖 ${s.name}`);
+      if (desc) console.log(`     ${desc}`);
+      console.log('');
+    }
+    if (scored.length > 10) {
+      console.log(`  ... 他 ${scored.length - 10} 件`);
+    }
+    console.log(`合計 ${scored.length} 件がヒットしました。`);
+    console.log('詳細は `satori skill info <name>` で確認できます。');
+  }
+}
+
+function skillInfo() {
+  const name = process.argv[4];
+  if (!name) {
+    console.error('Error: スキル名を指定してください。');
+    console.log('Usage: satori skill info <name>');
+    console.log('スキル検索は `satori skill search <query>` を使ってください。');
+    process.exit(1);
+  }
+
+  const skillsDir = path.join(SOURCE_DIR, 'skills');
+  // scientific- プレフィックスを自動補完
+  const dirName = name.startsWith('scientific-') ? name : `scientific-${name}`;
+  const filePath = path.join(skillsDir, dirName, 'SKILL.md');
+
+  if (!fs.existsSync(filePath)) {
+    console.error(`Error: スキル "${name}" が見つかりません。`);
+    console.log('');
+    // 部分一致候補を提示
+    if (fs.existsSync(skillsDir)) {
+      const dirs = fs
+        .readdirSync(skillsDir)
+        .filter((d) => d.startsWith('scientific-') && d.includes(name))
+        .slice(0, 5);
+      if (dirs.length > 0) {
+        console.log('もしかして:');
+        for (const d of dirs) {
+          console.log(`  - ${d.replace('scientific-', '')}`);
+        }
+      }
+    }
+    process.exit(1);
+  }
+
+  const content = fs.readFileSync(filePath, 'utf-8');
+  const fm = parseFrontmatter(content);
+  const h1Match = content.match(/^# (.+)$/m);
+  const title = h1Match ? h1Match[1].trim() : dirName;
+
+  // 説明抽出
+  const descMatch = content.match(/^description:\s*\|?\s*\n([\s\S]*?)(?=\n\w|\n---)/m);
+  const description = descMatch ? descMatch[1].replace(/^\s+/gm, '').trim() : '';
+
+  // When to Use セクション抽出
+  const whenMatch = content.match(/^## When to Use\s*\n([\s\S]*?)(?=\n## )/m);
+  const whenToUse = whenMatch ? whenMatch[1].trim() : '';
+
+  // TU ツール
+  const tuKeyPattern = /`([A-Z][a-zA-Z]*_[a-z]+_[a-z_]+)`/g;
+  const tuKeys = new Set();
+  for (const m of content.matchAll(tuKeyPattern)) {
+    tuKeys.add(m[1]);
+  }
+
+  // tu_tools from frontmatter
+  const tuToolMatches = content.match(/^tu_tools:\s*\n([\s\S]*?)(?=\n---|\n[a-z])/m);
+  const tuToolNames = [];
+  if (tuToolMatches) {
+    const toolLines = tuToolMatches[1].matchAll(/name:\s*(.+)/g);
+    for (const m of toolLines) {
+      tuToolNames.push(m[1].trim());
+    }
+  }
+
+  // 関連パイプライン
+  const shortName = dirName.replace('scientific-', '');
+  const relatedPipelines = PIPELINES.filter((p) => p.skills.includes(shortName));
+
+  console.log(`\n📖 ${title}`);
+  console.log(`   名前: ${fm?.name || dirName}`);
+  if (description) {
+    console.log(`   説明: ${description}`);
+  }
+  console.log('');
+
+  if (whenToUse) {
+    console.log('── When to Use ──');
+    console.log(whenToUse);
+    console.log('');
+  }
+
+  if (tuKeys.size > 0 || tuToolNames.length > 0) {
+    console.log('── ToolUniverse 連携 ──');
+    if (tuToolNames.length > 0) {
+      for (const t of tuToolNames) {
+        console.log(`  🔧 ${t}`);
+      }
+    }
+    if (tuKeys.size > 0) {
+      console.log(`  TU キー: ${[...tuKeys].join(', ')}`);
+    }
+    console.log('');
+  }
+
+  if (relatedPipelines.length > 0) {
+    console.log('── 関連パイプライン ──');
+    for (const p of relatedPipelines.slice(0, 5)) {
+      console.log(`  📋 #${p.id}: ${p.name}`);
+    }
+    if (relatedPipelines.length > 5) {
+      console.log(`  ... 他 ${relatedPipelines.length - 5} 件`);
+    }
+    console.log('');
+  }
+
+  console.log(`ファイル: src/.github/skills/${dirName}/SKILL.md`);
+}
+
 switch (COMMAND) {
   case 'init':
     init();
     break;
+  case 'skill':
+    if (SUBCOMMAND === 'search') {
+      skillSearch();
+    } else if (SUBCOMMAND === 'info') {
+      skillInfo();
+    } else {
+      console.error(`Unknown skill subcommand: ${SUBCOMMAND || '(none)'}`);
+      console.log('Usage: satori skill search <query> | satori skill info <name>');
+      process.exit(1);
+    }
+    break;
   case 'pipeline':
     if (SUBCOMMAND === 'suggest') {
       pipelineSuggest();
@@ -199,6 +921,12 @@ switch (COMMAND) {
       process.exit(1);
     }
     break;
+  case 'validate':
+    validate();
+    break;
+  case 'stats':
+    stats();
+    break;
   case 'help':
   case '--help':
   case '-h':