@nahisaho/satori 0.16.0 → 0.18.0

package/src/.github/skills/scientific-icgc-cancer-data/SKILL.md

@@ -0,0 +1,351 @@
+---
+name: scientific-icgc-cancer-data
+description: |
+  ICGC がんゲノムデータスキル。ICGC ARGO DCC API および
+  レガシー API による国際がんゲノムデータ検索・ドナー/
+  検体/変異解析。直接 API (ToolUniverse 非連携)。
+tu_tools: []
+---
+
+# Scientific ICGC Cancer Data
+
+ICGC (International Cancer Genome Consortium) ARGO DCC API を
+活用した国際がんゲノムデータ検索・変異統計・がん種横断解析
+パイプラインを提供する。
+
+## When to Use
+
+- 国際がんゲノムプロジェクトのデータを検索するとき
+- がん種ごとの体細胞変異プロファイルを調べるとき
+- ドナー・検体・変異の統計情報を取得するとき
+- がんゲノムの変異シグネチャを分析するとき
+- PCAWG (Pan-Cancer Analysis of Whole Genomes) データを活用するとき
+- がん遺伝子変異の国際比較データが必要なとき
+
+---
+
+## Quick Start
+
+## 1. ICGC プロジェクト・ドナー検索
+
+```python
+import requests
+import pandas as pd
+
+ICGC_BASE = "https://dcc.icgc.org/api/v1"
+
+
+def icgc_search_projects(query=None, limit=50):
+    """
+    ICGC — がんゲノムプロジェクト検索。
+
+    Parameters:
+        query: str — 検索キーワード (例: "lung", "BRCA")
+        limit: int — 最大結果数
+    """
+    url = f"{ICGC_BASE}/projects"
+    params = {"size": limit, "from": 1}
+    if query:
+        params["filters"] = (
+            f'{{"project":{{"primarySite":'
+            f'{{"is":["{query}"]}}}}}}'
+        )
+
+    resp = requests.get(url, params=params, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    results = []
+    for hit in data.get("hits", []):
+        results.append({
+            "project_id": hit.get("id", ""),
+            "project_name": hit.get("name", ""),
+            "primary_site": hit.get("primarySite", ""),
+            "tumour_type": hit.get("tumourType", ""),
+            "tumour_subtype": hit.get("tumourSubtype", ""),
+            "primary_country": "; ".join(
+                hit.get("primaryCountries", [])),
+            "total_donors": hit.get("totalDonorCount", 0),
+            "ssm_count": hit.get("ssmCount", 0),
+        })
+
+    df = pd.DataFrame(results)
+    if not df.empty:
+        df = df.sort_values("total_donors", ascending=False)
+
+    total = data.get("pagination", {}).get("total", 0)
+    print(f"ICGC projects: {len(df)}/{total} "
+          f"(query='{query}')")
+    return df
+
+
+def icgc_search_donors(project_id, limit=100):
+    """
+    ICGC — プロジェクト内ドナー検索。
+
+    Parameters:
+        project_id: str — プロジェクト ID (例: "BRCA-US")
+        limit: int — 最大結果数
+    """
+    url = f"{ICGC_BASE}/donors"
+    params = {
+        "size": limit,
+        "filters": (
+            f'{{"donor":{{"projectId":'
+            f'{{"is":["{project_id}"]}}}}}}'
+        ),
+    }
+
+    resp = requests.get(url, params=params, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    results = []
+    for hit in data.get("hits", []):
+        results.append({
+            "donor_id": hit.get("id", ""),
+            "project_id": project_id,
+            "primary_site": hit.get("primarySite", ""),
+            "gender": hit.get("gender", ""),
+            "vital_status": hit.get("vitalStatus", ""),
+            "age_at_diagnosis": hit.get("ageAtDiagnosis"),
+            "disease_status": hit.get(
+                "diseaseStatusLastFollowup", ""),
+            "ssm_count": hit.get("ssmCount", 0),
+        })
+
+    df = pd.DataFrame(results)
+    total = data.get("pagination", {}).get("total", 0)
+    print(f"ICGC donors: {len(df)}/{total} "
+          f"(project={project_id})")
+    return df
+```
+
+## 2. 体細胞変異 (SSM) 検索
+
+```python
+def icgc_search_mutations(gene_symbol=None,
+                             project_id=None,
+                             consequence_type=None,
+                             limit=100):
+    """
+    ICGC — 体細胞変異 (Simple Somatic Mutation) 検索。
+
+    Parameters:
+        gene_symbol: str — 遺伝子シンボル (例: "TP53")
+        project_id: str — プロジェクト ID
+        consequence_type: str — 変異タイプ
+            (例: "missense_variant")
+        limit: int — 最大結果数
+    """
+    url = f"{ICGC_BASE}/mutations"
+    filters = {}
+
+    if gene_symbol:
+        filters["gene"] = {"symbol": {"is": [gene_symbol]}}
+    if project_id:
+        filters["donor"] = {"projectId": {"is": [project_id]}}
+    if consequence_type:
+        filters["mutation"] = {
+            "consequenceType": {"is": [consequence_type]}
+        }
+
+    import json
+    params = {
+        "size": limit,
+        "filters": json.dumps(filters) if filters else "{}",
+    }
+
+    resp = requests.get(url, params=params, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    results = []
+    for hit in data.get("hits", []):
+        # 主要な consequence 取得
+        consequences = hit.get("consequences", [])
+        top_cons = consequences[0] if consequences else {}
+
+        results.append({
+            "mutation_id": hit.get("id", ""),
+            "chromosome": hit.get("chromosome", ""),
+            "start": hit.get("start"),
+            "end": hit.get("end"),
+            "mutation": hit.get("mutation", ""),
+            "type": hit.get("type", ""),
+            "gene_symbol": top_cons.get("geneSymbol", ""),
+            "consequence_type": top_cons.get("type", ""),
+            "aa_mutation": top_cons.get("aaMutation", ""),
+            "affected_donors": hit.get(
+                "affectedDonorCountTotal", 0),
+            "affected_projects": hit.get(
+                "affectedProjectCount", 0),
+            "functional_impact": hit.get(
+                "functionalImpact", ""),
+        })
+
+    df = pd.DataFrame(results)
+    if not df.empty:
+        df = df.sort_values("affected_donors",
+                            ascending=False)
+
+    total = data.get("pagination", {}).get("total", 0)
+    print(f"ICGC mutations: {len(df)}/{total} "
+          f"(gene={gene_symbol}, project={project_id})")
+    return df
+```
+
+## 3. がん種統計・変異サマリー
+
+```python
+def icgc_cancer_stats(project_id=None):
+    """
+    ICGC — がん種統計サマリー。
+
+    Parameters:
+        project_id: str — プロジェクト ID (None で全体統計)
+    """
+    if project_id:
+        url = f"{ICGC_BASE}/projects/{project_id}"
+        resp = requests.get(url, timeout=30)
+        resp.raise_for_status()
+        data = resp.json()
+
+        stats = {
+            "project_id": project_id,
+            "project_name": data.get("name", ""),
+            "primary_site": data.get("primarySite", ""),
+            "total_donors": data.get("totalDonorCount", 0),
+            "total_specimens": data.get(
+                "totalSpecimenCount", 0),
+            "ssm_count": data.get("ssmCount", 0),
+            "repository": "; ".join(
+                data.get("repository", [])),
+        }
+        print(f"ICGC stats: {project_id} — "
+              f"{stats['total_donors']} donors, "
+              f"{stats['ssm_count']} mutations")
+        return stats
+    else:
+        # 全プロジェクト概要
+        projects = icgc_search_projects(limit=200)
+        summary = {
+            "total_projects": len(projects),
+            "total_donors": projects[
+                "total_donors"].sum(),
+            "total_ssm": projects["ssm_count"].sum(),
+            "top_sites": projects.groupby(
+                "primary_site")["total_donors"].sum(
+                ).sort_values(ascending=False).head(10
+                ).to_dict(),
+        }
+        print(f"ICGC summary: {summary['total_projects']} "
+              f"projects, {summary['total_donors']} donors")
+        return summary
+
+
+def icgc_gene_mutation_frequency(gene_symbol, top_n=20):
+    """
+    ICGC — 遺伝子別がん種変異頻度。
+
+    Parameters:
+        gene_symbol: str — 遺伝子シンボル
+        top_n: int — 上位がん種数
+    """
+    mutations = icgc_search_mutations(
+        gene_symbol=gene_symbol, limit=500)
+
+    if mutations.empty:
+        return pd.DataFrame()
+
+    # プロジェクト別集計
+    freq = mutations.groupby("gene_symbol").agg(
+        total_mutations=("mutation_id", "count"),
+        total_affected_donors=("affected_donors", "sum"),
+        mutation_types=("consequence_type",
+                        lambda x: "; ".join(x.unique()[:5])),
+    ).reset_index()
+
+    print(f"ICGC gene frequency: {gene_symbol} — "
+          f"{len(freq)} entries")
+    return freq
+```
+
+## 4. ICGC 統合パイプライン
+
+```python
+def icgc_pipeline(gene_symbols, cancer_site=None,
+                     output_dir="results"):
+    """
+    ICGC 統合パイプライン。
+
+    Parameters:
+        gene_symbols: list[str] — 遺伝子リスト
+        cancer_site: str — がん部位フィルタ
+        output_dir: str — 出力ディレクトリ
+    """
+    from pathlib import Path
+    output_dir = Path(output_dir)
+    output_dir.mkdir(parents=True, exist_ok=True)
+
+    # 1) プロジェクト検索
+    projects = icgc_search_projects(query=cancer_site)
+    projects.to_csv(output_dir / "projects.csv", index=False)
+
+    # 2) 遺伝子別変異検索
+    all_mutations = []
+    for gene in gene_symbols:
+        try:
+            muts = icgc_search_mutations(
+                gene_symbol=gene, limit=200)
+            muts["query_gene"] = gene
+            all_mutations.append(muts)
+        except Exception as e:
+            print(f"  Warning: {gene} — {e}")
+            continue
+
+    if all_mutations:
+        combined = pd.concat(all_mutations,
+                              ignore_index=True)
+        combined.to_csv(output_dir / "mutations.csv",
+                        index=False)
+
+    # 3) がん種統計
+    if not projects.empty:
+        top_project = projects.iloc[0]["project_id"]
+        stats = icgc_cancer_stats(project_id=top_project)
+        pd.DataFrame([stats]).to_csv(
+            output_dir / "cancer_stats.csv", index=False)
+
+    print(f"ICGC pipeline: {output_dir}")
+    return {"projects": projects}
+```
+
+---
+
+## ToolUniverse 連携
+
+| TU Key | ツール名 | 連携内容 |
+|--------|---------|---------|
+| (direct) | ICGC DCC API | 直接 REST API — TU 非連携 |
+
+## パイプライン統合
+
+```
+cancer-genomics → icgc-cancer-data → precision-oncology
+  (がんゲノム全般)  (ICGC DCC API)   (精密腫瘍学)
+       │                 │                 ↓
+  tcga-data ────────────┘        clinical-decision-support
+  (TCGA データ)      │            (臨床意思決定)
+                     ↓
+          variant-interpretation
+          (変異臨床解釈)
+```
+
+## パイプライン出力
+
+| ファイル | 説明 | 次スキル |
+|---------|------|---------|
+| `results/projects.csv` | プロジェクト一覧 | → cancer-genomics |
+| `results/mutations.csv` | 体細胞変異 | → variant-interpretation |
+| `results/cancer_stats.csv` | がん種統計 | → precision-oncology |

package/src/.github/skills/scientific-metabolic-atlas/SKILL.md

@@ -0,0 +1,263 @@
+---
+name: scientific-metabolic-atlas
+description: |
+  代謝アトラススキル。Metabolic Atlas / Human-GEM REST API による
+  代謝反応・代謝産物・コンパートメント検索、フラックス解析統合、
+  代謝ネットワーク可視化。K-Dense 連携: metabolic-atlas。
+tu_tools: []
+kdense_ref: metabolic-atlas
+---
+
+# Scientific Metabolic Atlas
+
+Metabolic Atlas REST API を活用したゲノムスケール代謝モデル
+(GEM) 解析パイプラインを提供する。
+
+## When to Use
+
+- ヒト代謝反応・代謝産物を検索するとき
+- Human-GEM のコンパートメント情報を取得するとき
+- 代謝経路のネットワーク構造を解析するとき
+- フラックスバランス解析 (FBA) の入力を準備するとき
+- 代謝産物コネクティビティを可視化するとき
+- 組織特異的代謝モデルを構築するとき
+
+---
+
+## Quick Start
+
+## 1. 代謝反応検索
+
+```python
+import requests
+import pandas as pd
+import numpy as np
+
+MA_BASE = "https://metabolicatlas.org/api/v2"
+
+
+def metabolic_atlas_search_reactions(query, model="Human-GEM",
+                                       compartment=None, limit=50):
+    """
+    Metabolic Atlas — 代謝反応検索。
+
+    Parameters:
+        query: str — 検索クエリ (例: "glycolysis", "citrate")
+        model: str — GEM モデル名
+        compartment: str — コンパートメント (例: "cytosol", "mitochondria")
+        limit: int — 最大結果数
+    """
+    url = f"{MA_BASE}/search"
+    params = {
+        "query": query,
+        "model": model,
+        "type": "reaction",
+        "limit": limit,
+    }
+    resp = requests.get(url, params=params, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    results = []
+    for r in data.get("results", data) if isinstance(data, dict) else data:
+        rxn = r if isinstance(r, dict) else {}
+        row = {
+            "reaction_id": rxn.get("id", ""),
+            "name": rxn.get("name", ""),
+            "equation": rxn.get("equation", ""),
+            "subsystem": rxn.get("subsystem", ""),
+            "compartment": rxn.get("compartment", ""),
+            "gene_rule": rxn.get("geneRule", ""),
+            "lower_bound": rxn.get("lowerBound", None),
+            "upper_bound": rxn.get("upperBound", None),
+        }
+        if compartment and compartment.lower() not in str(
+                row.get("compartment", "")).lower():
+            continue
+        results.append(row)
+
+    df = pd.DataFrame(results[:limit])
+    print(f"Metabolic Atlas reactions: {len(df)} results "
+          f"(query={query})")
+    return df
+```
+
+## 2. 代謝産物検索
+
+```python
+def metabolic_atlas_search_metabolites(query, model="Human-GEM",
+                                          limit=50):
+    """
+    Metabolic Atlas — 代謝産物検索。
+
+    Parameters:
+        query: str — 検索クエリ (例: "glucose", "ATP")
+        model: str — GEM モデル名
+        limit: int — 最大結果数
+    """
+    url = f"{MA_BASE}/search"
+    params = {
+        "query": query,
+        "model": model,
+        "type": "metabolite",
+        "limit": limit,
+    }
+    resp = requests.get(url, params=params, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    results = []
+    for m in data.get("results", data) if isinstance(data, dict) else data:
+        met = m if isinstance(m, dict) else {}
+        results.append({
+            "metabolite_id": met.get("id", ""),
+            "name": met.get("name", ""),
+            "formula": met.get("formula", ""),
+            "charge": met.get("charge", None),
+            "compartment": met.get("compartment", ""),
+            "chebi_id": met.get("chebiId", ""),
+            "kegg_id": met.get("keggId", ""),
+        })
+
+    df = pd.DataFrame(results[:limit])
+    print(f"Metabolic Atlas metabolites: {len(df)} results "
+          f"(query={query})")
+    return df
+```
+
+## 3. 代謝ネットワーク解析
+
+```python
+import networkx as nx
+
+
+def metabolic_atlas_network(subsystem, model="Human-GEM"):
+    """
+    Metabolic Atlas — サブシステム代謝ネットワーク構築。
+
+    Parameters:
+        subsystem: str — サブシステム名 (例: "Glycolysis")
+        model: str — GEM モデル名
+    """
+    reactions = metabolic_atlas_search_reactions(
+        subsystem, model=model, limit=200)
+
+    G = nx.DiGraph()
+
+    for _, rxn in reactions.iterrows():
+        rxn_id = rxn["reaction_id"]
+        equation = str(rxn.get("equation", ""))
+
+        # 簡易パーサ: "A + B => C + D"
+        if "=>" in equation:
+            substrates_str, products_str = equation.split("=>", 1)
+        elif "=" in equation:
+            substrates_str, products_str = equation.split("=", 1)
+        else:
+            continue
+
+        substrates = [s.strip() for s in substrates_str.split("+")
+                       if s.strip()]
+        products = [p.strip() for p in products_str.split("+")
+                     if p.strip()]
+
+        G.add_node(rxn_id, type="reaction",
+                    name=rxn.get("name", ""))
+
+        for s in substrates:
+            G.add_node(s, type="metabolite")
+            G.add_edge(s, rxn_id)
+
+        for p in products:
+            G.add_node(p, type="metabolite")
+            G.add_edge(rxn_id, p)
+
+    # ネットワーク統計
+    n_reactions = sum(1 for _, d in G.nodes(data=True)
+                      if d.get("type") == "reaction")
+    n_metabolites = sum(1 for _, d in G.nodes(data=True)
+                         if d.get("type") == "metabolite")
+
+    print(f"Metabolic network: {n_reactions} reactions, "
+          f"{n_metabolites} metabolites, {G.number_of_edges()} edges")
+    return G
+```
+
+## 4. 代謝アトラス統合パイプライン
+
+```python
+def metabolic_atlas_pipeline(query, model="Human-GEM",
+                               output_dir="results"):
+    """
+    代謝アトラス統合パイプライン。
+
+    Parameters:
+        query: str — 代謝経路/サブシステム名
+        model: str — GEM モデル名
+        output_dir: str — 出力ディレクトリ
+    """
+    from pathlib import Path
+    output_dir = Path(output_dir)
+    output_dir.mkdir(parents=True, exist_ok=True)
+
+    # 1) 反応検索
+    reactions = metabolic_atlas_search_reactions(query, model=model)
+    reactions.to_csv(output_dir / "reactions.csv", index=False)
+
+    # 2) 代謝産物検索
+    metabolites = metabolic_atlas_search_metabolites(query, model=model)
+    metabolites.to_csv(output_dir / "metabolites.csv", index=False)
+
+    # 3) ネットワーク構築
+    G = metabolic_atlas_network(query, model=model)
+    nx.write_graphml(G, str(output_dir / "metabolic_network.graphml"))
+
+    # 4) ハブ代謝産物
+    met_nodes = [n for n, d in G.nodes(data=True)
+                  if d.get("type") == "metabolite"]
+    hub_scores = {n: G.degree(n) for n in met_nodes}
+    hub_df = pd.DataFrame([
+        {"metabolite": k, "degree": v}
+        for k, v in sorted(hub_scores.items(),
+                           key=lambda x: -x[1])[:20]
+    ])
+    hub_df.to_csv(output_dir / "hub_metabolites.csv", index=False)
+
+    print(f"Metabolic Atlas pipeline: {output_dir}")
+    return {
+        "reactions": reactions,
+        "metabolites": metabolites,
+        "network": G,
+        "hubs": hub_df,
+    }
+```
+
+---
+
+## K-Dense 連携
+
+| K-Dense Key | 参照内容 |
+|-------------|---------|
+| `metabolic-atlas` | 代謝モデル構造・反応データベース |
+
+## パイプライン統合
+
+```
+metabolic-modeling → metabolic-atlas → systems-biology
+  (COBRA/FBA)        (Human-GEM)       (統合モデリング)
+       │                   │                  ↓
+  pathway-enrichment ─────┘          gene-expression
+  (KEGG/Reactome)     │              (発現データ)
+                       ↓
+                 multi-omics
+                 (メタボロミクス統合)
+```
+
+## パイプライン出力
+
+| ファイル | 説明 | 次スキル |
+|---------|------|---------|
+| `results/reactions.csv` | 代謝反応一覧 | → metabolic-modeling |
+| `results/metabolites.csv` | 代謝産物一覧 | → pathway-enrichment |
+| `results/metabolic_network.graphml` | 代謝ネットワーク | → systems-biology |
+| `results/hub_metabolites.csv` | ハブ代謝産物 | → multi-omics |