@nahisaho/satori 0.11.0 → 0.12.0

package/src/.github/skills/scientific-cancer-genomics/SKILL.md

@@ -0,0 +1,287 @@
+---
+name: scientific-cancer-genomics
+description: |
+  がんゲノミクスポータル統合スキル。COSMIC (体細胞変異カタログ)、
+  cBioPortal (がんゲノミクスデータ解析)、DepMap (がん細胞依存性) の
+  3 大がんゲノミクスデータベースを統合した変異プロファイリング、
+  変異シグネチャー解析、遺伝子依存性 (essentiality) 評価、
+  コピー数変化・がん種横断解析パイプライン。
+  13 の ToolUniverse SMCP ツールと連携。
+---
+
+# Scientific Cancer Genomics
+
+COSMIC / cBioPortal / DepMap の 3 大がんゲノミクスポータルを統合した
+体細胞変異プロファイリング・機能解析パイプラインを提供する。
+
+## When to Use
+
+- がん関連遺伝子の体細胞変異をカタログ検索するとき
+- cBioPortal でがん種横断の遺伝子変異頻度を調べるとき
+- DepMap で遺伝子依存性 (essentiality) を評価するとき
+- 変異シグネチャー解析 (SBS/DBS/ID) を行うとき
+- コピー数変化 (CNA) のドライバー・パッセンジャー分類が必要なとき
+
+---
+
+## Quick Start
+
+## 1. COSMIC 体細胞変異検索
+
+```python
+import pandas as pd
+import numpy as np
+import requests
+
+
+def cosmic_search_mutations(gene, cancer_type=None, mutation_type=None):
+    """
+    COSMIC (Catalogue Of Somatic Mutations In Cancer) 変異検索。
+
+    Parameters:
+        gene: str — 遺伝子シンボル (e.g., "BRAF", "TP53")
+        cancer_type: str — がん種フィルタ (e.g., "melanoma")
+        mutation_type: str — 変異タイプ ("missense", "nonsense", "frameshift")
+    """
+    # ToolUniverse 経由: COSMIC_search_mutations, COSMIC_get_mutations_by_gene
+    # COSMIC API は認証が必要 (Academic 無料)
+
+    # Cancer Gene Census (CGC) チェック
+    cgc_genes = {
+        "TP53": {"role": "TSG", "tier": 1},
+        "BRAF": {"role": "oncogene", "tier": 1},
+        "KRAS": {"role": "oncogene", "tier": 1},
+        "EGFR": {"role": "oncogene", "tier": 1},
+        "PIK3CA": {"role": "oncogene", "tier": 1},
+        "BRCA1": {"role": "TSG", "tier": 1},
+        "BRCA2": {"role": "TSG", "tier": 1},
+        "ALK": {"role": "oncogene", "tier": 1},
+    }
+
+    gene_info = cgc_genes.get(gene.upper(), {})
+
+    result = {
+        "gene": gene,
+        "cgc_role": gene_info.get("role", "unknown"),
+        "cgc_tier": gene_info.get("tier", None),
+        "cancer_type_filter": cancer_type,
+        "mutation_type_filter": mutation_type,
+    }
+
+    print(f"COSMIC query: {gene} "
+          f"(CGC: {gene_info.get('role', 'N/A')}, "
+          f"Tier {gene_info.get('tier', 'N/A')})")
+    return result
+```
+
+## 2. cBioPortal がんゲノミクスデータ取得
+
+```python
+def cbioportal_query(genes, study_id=None, cancer_type=None,
+                      data_types=None):
+    """
+    cBioPortal REST API によるがんゲノミクスデータ取得。
+
+    Parameters:
+        genes: list — 遺伝子シンボルリスト
+        study_id: str — cBioPortal 研究 ID (e.g., "tcga_brca_pan_can_atlas_2018")
+        cancer_type: str — がん種 (e.g., "Breast Cancer")
+        data_types: list — ["mutations", "cna", "mrna", "methylation"]
+    """
+    base_url = "https://www.cbioportal.org/api"
+
+    if data_types is None:
+        data_types = ["mutations", "cna"]
+
+    results = {}
+
+    # 研究一覧取得
+    if study_id is None:
+        resp = requests.get(f"{base_url}/studies")
+        studies = resp.json()
+        if cancer_type:
+            studies = [s for s in studies
+                       if cancer_type.lower() in
+                       s.get("cancerType", {}).get("name", "").lower()]
+        print(f"cBioPortal: {len(studies)} studies for '{cancer_type}'")
+        results["studies"] = pd.DataFrame([{
+            "study_id": s["studyId"],
+            "name": s["name"],
+            "cancer_type": s.get("cancerType", {}).get("name", ""),
+            "sample_count": s.get("allSampleCount", 0),
+        } for s in studies[:20]])
+    else:
+        # 変異データ取得
+        if "mutations" in data_types:
+            url = f"{base_url}/molecular-profiles/{study_id}_mutations/mutations"
+            params = {"projection": "DETAILED"}
+            resp = requests.get(url, params=params)
+            if resp.status_code == 200:
+                mutations = resp.json()
+                mut_df = pd.DataFrame([{
+                    "gene": m.get("gene", {}).get("hugoGeneSymbol", ""),
+                    "mutation": m.get("proteinChange", ""),
+                    "mutation_type": m.get("mutationType", ""),
+                    "chromosome": m.get("chr", ""),
+                    "position": m.get("startPosition", ""),
+                    "allele_freq": m.get("tumorAltCount", 0) /
+                                   max(m.get("tumorRefCount", 1) +
+                                       m.get("tumorAltCount", 1), 1),
+                } for m in mutations
+                    if m.get("gene", {}).get("hugoGeneSymbol", "") in genes])
+                results["mutations"] = mut_df
+                print(f"  Mutations: {len(mut_df)} found in {genes}")
+
+    return results
+```
+
+## 3. DepMap 遺伝子依存性解析
+
+```python
+def depmap_gene_dependency(genes, cell_lineage=None):
+    """
+    DepMap (Cancer Dependency Map) 遺伝子依存性解析。
+
+    Parameters:
+        genes: list — 遺伝子シンボルリスト
+        cell_lineage: str — 細胞系統フィルタ (e.g., "Lung", "Breast")
+    """
+    # ToolUniverse 経由:
+    # DepMap_search_genes, DepMap_get_gene_dependencies
+    # DepMap_get_cell_line, DepMap_get_cell_lines, DepMap_search_cell_lines
+
+    # DepMap CRISPR (Chronos) dependency score:
+    # negative = essential (依存), ~0 = non-essential
+    # Common Essential: mean < -0.5 across 90% of lines
+    # Selective Dependency: mean < -0.5 in specific lineages
+
+    results = []
+    for gene in genes:
+        result = {
+            "gene": gene,
+            "cell_lineage": cell_lineage,
+            "query_type": "CRISPR_dependency",
+            # 実際のスコアは ToolUniverse 経由で取得
+            "interpretation": (
+                "Chronos score < 0: gene essentiality increases. "
+                "score < -0.5: likely essential in this lineage. "
+                "score ~ 0: non-essential."
+            ),
+        }
+        results.append(result)
+
+    df = pd.DataFrame(results)
+    print(f"DepMap: queried {len(genes)} genes "
+          f"(lineage: {cell_lineage or 'pan-cancer'})")
+    return df
+```
+
+## 4. 変異シグネチャー解析
+
+```python
+def mutational_signature_analysis(mutations_df, genome="GRCh38",
+                                    n_signatures=None):
+    """
+    体細胞変異シグネチャー解析 (COSMIC SBS signatures)。
+
+    Parameters:
+        mutations_df: DataFrame — columns: [chr, pos, ref, alt, sample]
+        genome: str — 参照ゲノム
+        n_signatures: int — 抽出シグネチャー数 (None=自動推定)
+    """
+    from itertools import product
+
+    # 96 トリヌクレオチドコンテキスト
+    bases = ["C", "T"]
+    contexts = []
+    for ref in bases:
+        for alt in ["A", "C", "G", "T"]:
+            if ref == alt:
+                continue
+            for five in "ACGT":
+                for three in "ACGT":
+                    contexts.append(f"{five}[{ref}>{alt}]{three}")
+
+    # サンプルごとのカタログ構築
+    samples = mutations_df["sample"].unique()
+    catalog = pd.DataFrame(0, index=contexts, columns=samples)
+
+    for _, row in mutations_df.iterrows():
+        ref = row["ref"]
+        alt = row["alt"]
+        sample = row["sample"]
+        context = row.get("trinucleotide_context", "N[N>N]N")
+        if context in catalog.index:
+            catalog.loc[context, sample] += 1
+
+    print(f"Mutation catalog: {len(contexts)} contexts, "
+          f"{len(samples)} samples, "
+          f"{catalog.sum().sum():.0f} total mutations")
+
+    # NMF 分解 (SigProfilerExtractor 代替)
+    from sklearn.decomposition import NMF
+
+    X = catalog.values.T  # samples × contexts
+    if n_signatures is None:
+        n_signatures = min(5, len(samples))
+
+    model = NMF(n_components=n_signatures, random_state=42, max_iter=1000)
+    W = model.fit_transform(X)  # exposure matrix
+    H = model.components_  # signature profiles
+
+    signatures = pd.DataFrame(H.T, index=contexts,
+                               columns=[f"SBS_{i+1}" for i in range(n_signatures)])
+    exposures = pd.DataFrame(W, index=samples,
+                              columns=[f"SBS_{i+1}" for i in range(n_signatures)])
+
+    print(f"Extracted {n_signatures} mutational signatures")
+    return signatures, exposures
+```
+
+## References
+
+### Output Files
+
+| ファイル | 形式 |
+|---|---|
+| `results/cosmic_mutations.csv` | CSV |
+| `results/cbioportal_mutations.csv` | CSV |
+| `results/depmap_dependencies.csv` | CSV |
+| `results/mutation_signatures.csv` | CSV |
+| `results/signature_exposures.csv` | CSV |
+| `figures/mutation_spectrum.png` | PNG |
+| `figures/signature_profiles.png` | PNG |
+
+### 利用可能ツール
+
+> [ToolUniverse](https://github.com/mims-harvard/ToolUniverse) SMCP 経由で利用可能な外部ツール。
+
+| カテゴリ | 主要ツール | 用途 |
+|---|---|---|
+| COSMIC | `COSMIC_search_mutations` | 体細胞変異検索 |
+| COSMIC | `COSMIC_get_mutations_by_gene` | 遺伝子別変異取得 |
+| cBioPortal | `cBioPortal_get_cancer_studies` | がん研究一覧 |
+| cBioPortal | `cBioPortal_get_mutations` | 変異データ取得 |
+| cBioPortal | `cBioPortal_get_molecular_profiles` | 分子プロファイル |
+| cBioPortal | `cBioPortal_get_patients` | 患者データ取得 |
+| cBioPortal | `cBioPortal_get_sample_lists` | サンプルリスト |
+| cBioPortal | `cBioPortal_get_samples` | サンプル詳細 |
+| DepMap | `DepMap_get_gene_dependencies` | 遺伝子依存性スコア |
+| DepMap | `DepMap_get_cell_line` | 細胞株情報 |
+| DepMap | `DepMap_get_cell_lines` | 細胞株一覧 |
+| DepMap | `DepMap_search_cell_lines` | 細胞株検索 |
+| DepMap | `DepMap_search_genes` | 遺伝子検索 |
+
+### 参照スキル
+
+| スキル | 関連 |
+|---|---|
+| `scientific-precision-oncology` | 腫瘍プロファイル → 治療選択 |
+| `scientific-variant-interpretation` | バリアント臨床解釈 |
+| `scientific-variant-effect-prediction` | 計算病原性予測 |
+| `scientific-disease-research` | GWAS → がんリスク |
+| `scientific-drug-target-profiling` | 標的同定 → 依存性 |
+
+### 依存パッケージ
+
+`pandas`, `numpy`, `requests`, `scikit-learn`, `matplotlib`

package/src/.github/skills/scientific-clinical-decision-support/SKILL.md

@@ -300,3 +300,5 @@ Clinical decisions must be made by qualified healthcare professionals.
 | `scientific-deep-research` | ← 最新エビデンスの収集 |
 | `scientific-presentation-design` | → 臨床結果のプレゼンテーション |
 | `scientific-academic-writing` | → 研究成果の論文化 |
+| `scientific-clinical-trials-analytics` | ← 臨床試験マッチング・競合解析 |
+| `scientific-pharmacogenomics` | ← PGx バイオマーカー・投与量調整 |

package/src/.github/skills/scientific-clinical-reporting/SKILL.md

@@ -0,0 +1,324 @@
+---
+name: scientific-clinical-reporting
+description: |
+  臨床レポート自動生成スキル。検査結果サマリー (SOAP ノート)、バイオマーカー
+  プロファイルレポート、薬理ゲノミクスレポート、臨床試験要約を構造化テンプレート
+  (PDF/LaTeX/HTML) で出力。HL7 FHIR DiagnosticReport 形式にも対応。
+---
+
+# Scientific Clinical Reporting
+
+臨床データから構造化レポートを自動生成するパイプラインを提供する。
+
+## When to Use
+
+- 検査結果を SOAP ノート形式でまとめるとき
+- バイオマーカープロファイルレポートを作成するとき
+- ファーマコゲノミクスレポート (CPIC ガイドライン準拠) が必要なとき
+- 臨床試験の CSR (Clinical Study Report) サマリーを生成するとき
+- HL7 FHIR DiagnosticReport 形式で出力するとき
+
+---
+
+## Quick Start
+
+## 1. SOAP ノート生成
+
+```python
+import json
+from datetime import datetime
+
+
+def generate_soap_note(patient_data, findings, assessment, plan):
+    """
+    SOAP ノート形式の臨床レポートを生成。
+
+    Parameters:
+        patient_data: dict — {"id": "...", "age": 45, "sex": "M", ...}
+        findings: dict — {"subjective": [...], "objective": [...]}
+        assessment: list — 評価・診断リスト
+        plan: list — 治療計画リスト
+    """
+    soap = {
+        "report_type": "SOAP_Note",
+        "generated_at": datetime.now().isoformat(),
+        "patient": {
+            "id": patient_data.get("id", "ANON"),
+            "age": patient_data.get("age"),
+            "sex": patient_data.get("sex"),
+        },
+        "S": {  # Subjective
+            "chief_complaint": findings.get("chief_complaint", ""),
+            "history": findings.get("subjective", []),
+        },
+        "O": {  # Objective
+            "vitals": findings.get("vitals", {}),
+            "lab_results": findings.get("lab_results", []),
+            "imaging": findings.get("imaging", []),
+            "physical_exam": findings.get("objective", []),
+        },
+        "A": {  # Assessment
+            "diagnoses": assessment,
+            "differential": findings.get("differential", []),
+        },
+        "P": {  # Plan
+            "treatment": plan,
+            "follow_up": findings.get("follow_up", ""),
+            "referrals": findings.get("referrals", []),
+        },
+    }
+
+    print(f"SOAP note: patient={soap['patient']['id']}, "
+          f"diagnoses={len(assessment)}, plans={len(plan)}")
+    return soap
+```
+
+## 2. バイオマーカープロファイルレポート
+
+```python
+import pandas as pd
+
+
+def biomarker_profile_report(biomarkers_df, reference_ranges=None):
+    """
+    バイオマーカープロファイルレポート生成。
+
+    Parameters:
+        biomarkers_df: DataFrame — columns: [marker, value, unit, specimen]
+        reference_ranges: dict — {"marker": {"low": x, "high": y, "unit": "..."}}
+    """
+    if reference_ranges is None:
+        reference_ranges = {
+            "CEA": {"low": 0, "high": 5.0, "unit": "ng/mL"},
+            "AFP": {"low": 0, "high": 10.0, "unit": "ng/mL"},
+            "CA19-9": {"low": 0, "high": 37.0, "unit": "U/mL"},
+            "CA125": {"low": 0, "high": 35.0, "unit": "U/mL"},
+            "PSA": {"low": 0, "high": 4.0, "unit": "ng/mL"},
+            "HER2": {"low": 0, "high": 1, "unit": "IHC score"},
+            "Ki-67": {"low": 0, "high": 14, "unit": "%"},
+            "PD-L1 TPS": {"low": 0, "high": 1, "unit": "%"},
+        }
+
+    results = []
+    for _, row in biomarkers_df.iterrows():
+        marker = row["marker"]
+        value = float(row["value"])
+        ref = reference_ranges.get(marker, {})
+
+        status = "normal"
+        if ref:
+            if value > ref.get("high", float("inf")):
+                status = "HIGH"
+            elif value < ref.get("low", float("-inf")):
+                status = "LOW"
+
+        results.append({
+            "marker": marker,
+            "value": value,
+            "unit": row.get("unit", ref.get("unit", "")),
+            "reference": f"{ref.get('low', '?')}-{ref.get('high', '?')}",
+            "status": status,
+        })
+
+    report_df = pd.DataFrame(results)
+    abnormal = report_df[report_df["status"] != "normal"]
+
+    report = {
+        "report_type": "Biomarker_Profile",
+        "total_markers": len(report_df),
+        "abnormal_count": len(abnormal),
+        "results": report_df.to_dict("records"),
+        "summary": (
+            f"{len(abnormal)} of {len(report_df)} markers outside reference range"
+            if len(abnormal) > 0
+            else "All markers within reference range"
+        ),
+    }
+
+    print(f"Biomarker profile: {len(report_df)} markers, "
+          f"{len(abnormal)} abnormal")
+    return report
+```
+
+## 3. ファーマコゲノミクスレポート
+
+```python
+def pharmacogenomics_report(genotypes, medications):
+    """
+    CPIC ガイドライン準拠のファーマコゲノミクスレポート。
+
+    Parameters:
+        genotypes: dict — {"CYP2D6": "*1/*4", "CYP2C19": "*1/*2", ...}
+        medications: list — ["codeine", "clopidogrel", ...]
+    """
+    # CPIC phenotype マッピング (簡略)
+    cpic_phenotypes = {
+        "CYP2D6": {
+            "*1/*1": "Normal Metabolizer",
+            "*1/*4": "Intermediate Metabolizer",
+            "*4/*4": "Poor Metabolizer",
+            "*1/*2xN": "Ultrarapid Metabolizer",
+        },
+        "CYP2C19": {
+            "*1/*1": "Normal Metabolizer",
+            "*1/*2": "Intermediate Metabolizer",
+            "*2/*2": "Poor Metabolizer",
+            "*1/*17": "Rapid Metabolizer",
+            "*17/*17": "Ultrarapid Metabolizer",
+        },
+    }
+
+    # 推奨アクション (簡略)
+    drug_gene_map = {
+        "codeine": {"gene": "CYP2D6", "action": {
+            "Poor Metabolizer": "AVOID — use alternative analgesic",
+            "Ultrarapid Metabolizer": "AVOID — toxicity risk",
+            "Intermediate Metabolizer": "Use with caution, consider alternative",
+        }},
+        "clopidogrel": {"gene": "CYP2C19", "action": {
+            "Poor Metabolizer": "Use alternative antiplatelet (e.g., prasugrel)",
+            "Intermediate Metabolizer": "Consider alternative antiplatelet",
+        }},
+    }
+
+    recommendations = []
+    for drug in medications:
+        entry = drug_gene_map.get(drug, {})
+        gene = entry.get("gene", "Unknown")
+        genotype = genotypes.get(gene, "Unknown")
+        phenotype_map = cpic_phenotypes.get(gene, {})
+        phenotype = phenotype_map.get(genotype, "Indeterminate")
+
+        action = entry.get("action", {}).get(phenotype, "Standard dosing")
+        recommendations.append({
+            "drug": drug,
+            "gene": gene,
+            "genotype": genotype,
+            "phenotype": phenotype,
+            "recommendation": action,
+            "cpic_level": "A" if drug in drug_gene_map else "N/A",
+        })
+
+    report = {
+        "report_type": "Pharmacogenomics",
+        "genotypes_tested": genotypes,
+        "medications_queried": medications,
+        "recommendations": recommendations,
+    }
+
+    print(f"PGx report: {len(genotypes)} genes, {len(medications)} drugs, "
+          f"{len(recommendations)} recommendations")
+    return report
+```
+
+## 4. 構造化レポート出力 (LaTeX/HTML)
+
+```python
+def export_clinical_report(report, output_format="html",
+                            output_path="reports/clinical_report"):
+    """
+    臨床レポートを LaTeX/HTML/FHIR JSON 形式で出力。
+
+    Parameters:
+        report: dict — SOAP, Biomarker, PGx レポート
+        output_format: "html", "latex", "fhir_json"
+        output_path: str — 出力先パス (拡張子なし)
+    """
+    import os
+    os.makedirs(os.path.dirname(output_path), exist_ok=True)
+    report_type = report.get("report_type", "Clinical")
+
+    if output_format == "html":
+        filepath = f"{output_path}.html"
+        html_parts = [
+            "<!DOCTYPE html><html><head>",
+            f"<title>{report_type} Report</title>",
+            "<style>body{font-family:Arial;margin:2em;}"
+            "table{border-collapse:collapse;width:100%;}"
+            "td,th{border:1px solid #ddd;padding:8px;}</style>",
+            "</head><body>",
+            f"<h1>{report_type} Report</h1>",
+        ]
+
+        if report_type == "SOAP_Note":
+            for section in ["S", "O", "A", "P"]:
+                html_parts.append(f"<h2>{section}</h2>")
+                html_parts.append(f"<pre>{json.dumps(report.get(section, {}), indent=2, ensure_ascii=False)}</pre>")
+
+        elif report_type == "Biomarker_Profile":
+            html_parts.append("<table><tr><th>Marker</th><th>Value</th>"
+                              "<th>Reference</th><th>Status</th></tr>")
+            for r in report.get("results", []):
+                status_color = "red" if r["status"] != "normal" else "green"
+                html_parts.append(
+                    f"<tr><td>{r['marker']}</td><td>{r['value']} {r['unit']}</td>"
+                    f"<td>{r['reference']}</td>"
+                    f"<td style='color:{status_color}'>{r['status']}</td></tr>"
+                )
+            html_parts.append("</table>")
+
+        html_parts.append("</body></html>")
+        with open(filepath, "w") as f:
+            f.write("\n".join(html_parts))
+
+    elif output_format == "fhir_json":
+        filepath = f"{output_path}.fhir.json"
+        fhir = {
+            "resourceType": "DiagnosticReport",
+            "status": "final",
+            "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/v2-0074",
+                                       "code": "LAB"}]}],
+            "code": {"text": report_type},
+            "issued": report.get("generated_at", datetime.now().isoformat()),
+            "result": [],
+        }
+        with open(filepath, "w") as f:
+            json.dump(fhir, f, indent=2)
+
+    elif output_format == "latex":
+        filepath = f"{output_path}.tex"
+        with open(filepath, "w") as f:
+            f.write(f"\\documentclass{{article}}\n")
+            f.write(f"\\title{{{report_type} Report}}\n")
+            f.write("\\begin{document}\n\\maketitle\n")
+            f.write(f"Report type: {report_type}\n")
+            f.write("\\end{document}\n")
+
+    print(f"Report exported: {filepath}")
+    return filepath
+```
+
+## References
+
+### Output Files
+
+| ファイル | 形式 |
+|---|---|
+| `reports/soap_note.json` | JSON |
+| `reports/biomarker_profile.json` | JSON |
+| `reports/pgx_report.json` | JSON |
+| `reports/clinical_report.html` | HTML |
+| `reports/clinical_report.tex` | LaTeX |
+| `reports/clinical_report.fhir.json` | FHIR JSON |
+
+### 利用可能ツール
+
+> 本スキルは ToolUniverse ツールに直接依存しない。
+
+| カテゴリ | 主要ツール | 用途 |
+|---|---|---|
+| — | — | — |
+
+### 参照スキル
+
+| スキル | 関連 |
+|---|---|
+| `scientific-variant-interpretation` | バリアント解釈レポート |
+| `scientific-variant-effect-prediction` | バリアント病原性スコア |
+| `scientific-pharmacogenomics` | PGx ガイドライン |
+| `scientific-precision-oncology` | 精密腫瘍学レポート |
+| `scientific-disease-research` | 疾患情報統合 |
+
+### 依存パッケージ
+
+`pandas`, `json` (stdlib), `datetime` (stdlib)

package/src/.github/skills/scientific-computational-materials/SKILL.md

@@ -343,10 +343,10 @@ def parse_vasp_output(vasprun_file="vasprun.xml"):
 
 | スキル | 関連 |
 |---|---|
-| `scientific-quantum-chemistry` | DFT / 量子化学計算 |
-| `scientific-molecular-dynamics` | 分子動力学シミュレーション |
-| `scientific-visualization` | 構造可視化 |
-| `scientific-data-analysis` | 材料データ統計解析 |
+| `scientific-quantum-computing` | 量子計算・VQE・量子化学 |
+| `scientific-cheminformatics` | 分子記述子・構造解析 |
+| `scientific-publication-figures` | 構造・相図可視化 |
+| `scientific-materials-characterization` | XRD・SEM・実験材料特性 |
 
 ### 依存パッケージ
 

package/src/.github/skills/scientific-deep-learning/SKILL.md

@@ -373,3 +373,4 @@ def export_model(model, sample_input, export_dir="models"):
 | `scientific-image-analysis` | ← 画像データの CNN 応用 |
 | `scientific-medical-imaging` | → 医用画像の DL モデル |
 | `scientific-quantum-computing` | ← 量子-古典ハイブリッド ML |
+| `scientific-neuroscience-electrophysiology` | ← 神経デコーディング・スパイクソート DL |

package/src/.github/skills/scientific-epidemiology-public-health/SKILL.md

@@ -326,6 +326,7 @@ def blocks_all_backdoor(G, X, Y, Z):
 | [scientific-meta-analysis](../scientific-meta-analysis/SKILL.md) | メタアナリシス・系統的レビュー |
 | [scientific-infectious-disease](../scientific-infectious-disease/SKILL.md) | 感染症疫学 |
 | [scientific-bayesian-statistics](../scientific-bayesian-statistics/SKILL.md) | ベイズ空間モデル |
+| [scientific-clinical-trials-analytics](../scientific-clinical-trials-analytics/SKILL.md) | 臨床試験レジストリ |
 
 #### 依存パッケージ
 

package/src/.github/skills/scientific-grant-writing/SKILL.md

@@ -313,3 +313,5 @@ BUDGET_JUSTIFICATION_TEMPLATE = """
 | `scientific-hypothesis-pipeline` | ← 仮説定義・課題設定 |
 | `scientific-deep-research` | ← 文献レビュー・先行研究調査 |
 | `scientific-academic-writing` | ← アカデミックライティングスキル |
+| `scientific-scientific-schematics` | ← 研究計画図・フロー図生成 |
+| `scientific-regulatory-science` | ← 規制戦略セクション |

package/src/.github/skills/scientific-lab-data-management/SKILL.md

@@ -324,10 +324,10 @@ def fork_protocol(original_protocol_id, modifications):
 | スキル | 関連 |
 |---|---|
 | `scientific-bioinformatics` | ゲノミクスデータ解析 |
-| `scientific-imaging-analysis` | 顕微鏡画像解析 |
+| `scientific-image-analysis` | 顯微鏡画像解析 |
 | `scientific-gene-expression-transcriptomics` | RNA-seq データ管理 |
 | `scientific-single-cell-genomics` | scRNA-seq データ管理 |
-| `scientific-data-analysis` | データ前処理 |
+| `scientific-data-preprocessing` | データ前処理 |
 
 ### 依存パッケージ