@nahisaho/satori 0.18.0 → 0.20.0

package/src/.github/skills/scientific-drugbank-resources/SKILL.md

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+---
+name: scientific-drugbank-resources
+description: |
+  DrugBank リソーススキル。DrugBank API を用いた薬剤記述・
+  薬理情報・標的タンパク質・薬物相互作用検索。
+  ToolUniverse 連携: drugbank。
+tu_tools:
+  - key: drugbank
+    name: DrugBank
+    description: 薬剤データベース API
+---
+
+# Scientific DrugBank Resources
+
+DrugBank API を活用した薬剤記述・薬理情報 (MOA)・標的タンパク質
+検索・薬物相互作用 (DDI) パイプラインを提供する。
+
+## When to Use
+
+- 薬剤の基本情報 (名前・分類・構造) を検索するとき
+- 薬理メカニズム (MOA) を調べるとき
+- 標的タンパク質から薬剤を逆引き検索するとき
+- 薬物相互作用 (DDI) を確認するとき
+- 薬剤の ADMET プロパティを取得するとき
+
+---
+
+## Quick Start
+
+## 1. 薬剤検索・基本情報
+
+```python
+import requests
+import pandas as pd
+
+DRUGBANK_API = "https://api.drugbank.com/v1"
+
+
+def drugbank_search(query, limit=25, api_key=None):
+    """
+    DrugBank — 薬剤テキスト検索。
+
+    Parameters:
+        query: str — 検索クエリ (例: "imatinib")
+        limit: int — 最大結果数
+        api_key: str — DrugBank API キー
+    """
+    headers = {}
+    if api_key:
+        headers["Authorization"] = f"Bearer {api_key}"
+
+    url = f"{DRUGBANK_API}/drugs"
+    params = {"q": query, "per_page": limit}
+    resp = requests.get(url, params=params,
+                        headers=headers, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    rows = []
+    for d in data:
+        rows.append({
+            "drugbank_id": d.get("drugbank_id", ""),
+            "name": d.get("name", ""),
+            "cas_number": d.get("cas_number", ""),
+            "drug_type": d.get("type", ""),
+            "state": d.get("state", ""),
+            "description": (d.get("description", "")
+                            [:200]),
+        })
+
+    df = pd.DataFrame(rows)
+    print(f"DrugBank search: '{query}' → {len(df)} drugs")
+    return df
+
+
+def drugbank_drug_detail(drugbank_id, api_key=None):
+    """
+    DrugBank — 薬剤詳細取得。
+
+    Parameters:
+        drugbank_id: str — DrugBank ID (例: "DB01254")
+        api_key: str — DrugBank API キー
+    """
+    headers = {}
+    if api_key:
+        headers["Authorization"] = f"Bearer {api_key}"
+
+    url = f"{DRUGBANK_API}/drugs/{drugbank_id}"
+    resp = requests.get(url, headers=headers, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    result = {
+        "drugbank_id": data.get("drugbank_id", ""),
+        "name": data.get("name", ""),
+        "description": data.get("description", ""),
+        "indication": data.get("indication", ""),
+        "pharmacodynamics": data.get(
+            "pharmacodynamics", ""),
+        "mechanism_of_action": data.get(
+            "mechanism_of_action", ""),
+        "absorption": data.get("absorption", ""),
+        "half_life": data.get("half_life", ""),
+        "protein_binding": data.get(
+            "protein_binding", ""),
+        "molecular_weight": data.get(
+            "average_molecular_weight", ""),
+    }
+    return result
+```
+
+## 2. 標的タンパク質検索
+
+```python
+def drugbank_targets(drugbank_id, api_key=None):
+    """
+    DrugBank — 薬剤の標的タンパク質取得。
+
+    Parameters:
+        drugbank_id: str — DrugBank ID
+        api_key: str — DrugBank API キー
+    """
+    headers = {}
+    if api_key:
+        headers["Authorization"] = f"Bearer {api_key}"
+
+    url = f"{DRUGBANK_API}/drugs/{drugbank_id}/targets"
+    resp = requests.get(url, headers=headers, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    rows = []
+    for t in data:
+        polypeptide = t.get("polypeptide", {}) or {}
+        rows.append({
+            "drugbank_id": drugbank_id,
+            "target_name": t.get("name", ""),
+            "organism": t.get("organism", ""),
+            "known_action": t.get("known_action", ""),
+            "gene_name": polypeptide.get(
+                "gene_name", ""),
+            "uniprot_id": polypeptide.get(
+                "external_identifiers", {}).get(
+                "UniProtKB", ""),
+        })
+
+    df = pd.DataFrame(rows)
+    print(f"DrugBank targets: {drugbank_id} "
+          f"→ {len(df)} targets")
+    return df
+```
+
+## 3. 薬物相互作用 (DDI)
+
+```python
+def drugbank_interactions(drugbank_id, api_key=None):
+    """
+    DrugBank — 薬物相互作用取得。
+
+    Parameters:
+        drugbank_id: str — DrugBank ID
+        api_key: str — DrugBank API キー
+    """
+    headers = {}
+    if api_key:
+        headers["Authorization"] = f"Bearer {api_key}"
+
+    url = (f"{DRUGBANK_API}/drugs/"
+           f"{drugbank_id}/drug_interactions")
+    resp = requests.get(url, headers=headers, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    rows = []
+    for inter in data:
+        rows.append({
+            "drug_a": drugbank_id,
+            "drug_b_id": inter.get(
+                "drugbank_id", ""),
+            "drug_b_name": inter.get("name", ""),
+            "description": inter.get(
+                "description", "")[:300],
+        })
+
+    df = pd.DataFrame(rows)
+    print(f"DrugBank DDI: {drugbank_id} "
+          f"→ {len(df)} interactions")
+    return df
+```
+
+## 4. DrugBank 統合パイプライン
+
+```python
+def drugbank_pipeline(drug_name, api_key=None,
+                         output_dir="results"):
+    """
+    DrugBank 統合パイプライン。
+
+    Parameters:
+        drug_name: str — 薬剤名 (例: "imatinib")
+        api_key: str — DrugBank API キー
+        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) 検索
+    results = drugbank_search(drug_name,
+                              api_key=api_key)
+    results.to_csv(output_dir / "drugbank_search.csv",
+                   index=False)
+
+    if results.empty:
+        print(f"DrugBank: '{drug_name}' not found")
+        return {"search": results}
+
+    db_id = results.iloc[0]["drugbank_id"]
+
+    # 2) 詳細
+    detail = drugbank_drug_detail(db_id,
+                                  api_key=api_key)
+    pd.DataFrame([detail]).to_csv(
+        output_dir / "drugbank_detail.csv",
+        index=False)
+
+    # 3) 標的
+    targets = drugbank_targets(db_id,
+                               api_key=api_key)
+    targets.to_csv(output_dir / "drugbank_targets.csv",
+                   index=False)
+
+    # 4) DDI
+    ddi = drugbank_interactions(db_id,
+                                api_key=api_key)
+    ddi.to_csv(output_dir / "drugbank_ddi.csv",
+               index=False)
+
+    print(f"DrugBank pipeline: {drug_name} → {output_dir}")
+    return {"detail": detail, "targets": targets,
+            "ddi": ddi}
+```
+
+---
+
+## ToolUniverse 連携
+
+| TU Key | ツール名 | 連携内容 |
+|--------|---------|---------|
+| `drugbank` | DrugBank | 薬剤データベース API |
+
+## パイプライン統合
+
+```
+drug-target-profiling → drugbank-resources → admet-pharmacokinetics
+  (標的プロファイリング)   (DrugBank API)     (ADMET 予測)
+          │                     │                  ↓
+opentargets-genetics ──────────┘       compound-screening
+  (OT 薬剤エビデンス)                  (ZINC 化合物検索)
+```
+
+## パイプライン出力
+
+| ファイル | 説明 | 次スキル |
+|---------|------|---------|
+| `results/drugbank_search.csv` | 薬剤検索結果 | → drug-target-profiling |
+| `results/drugbank_detail.csv` | 薬剤詳細 | → admet-pharmacokinetics |
+| `results/drugbank_targets.csv` | 標的タンパク質 | → protein-interaction-network |
+| `results/drugbank_ddi.csv` | 薬物相互作用 | → pharmacogenomics |

package/src/.github/skills/scientific-gdc-portal/SKILL.md

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+---
+name: scientific-gdc-portal
+description: |
+  NCI Genomic Data Commons ポータルスキル。GDC REST API
+  を用いたがんゲノムプロジェクト横断検索・ケースメタデータ・
+  体細胞変異 (SSM)・遺伝子発現・ファイル取得。
+  ToolUniverse 連携: gdc。
+tu_tools:
+  - key: gdc
+    name: GDC
+    description: NCI Genomic Data Commons REST API
+---
+
+# Scientific GDC Portal
+
+NCI Genomic Data Commons (GDC) REST API を活用した
+がんゲノムプロジェクト横断検索・ケースメタデータ取得・
+体細胞変異 (SSM)・遺伝子発現パイプラインを提供する。
+
+## When to Use
+
+- TCGA/TARGET 等のがんゲノムデータを横断検索するとき
+- がん種別のケースメタデータを取得するとき
+- 特定遺伝子の体細胞変異 (SSM) 頻度を調べるとき
+- がんプロジェクトの統計サマリーを取得するとき
+- GDC ファイルメタデータを検索してダウンロード URL を取得するとき
+
+---
+
+## Quick Start
+
+## 1. プロジェクト検索・統計
+
+```python
+import requests
+import pandas as pd
+
+GDC_API = "https://api.gdc.cancer.gov"
+
+
+def gdc_projects(disease_type=None, limit=50):
+    """
+    GDC — プロジェクト検索。
+
+    Parameters:
+        disease_type: str — 疾患タイプフィルタ
+            (例: "Breast Invasive Carcinoma")
+        limit: int — 最大結果数
+    """
+    url = f"{GDC_API}/projects"
+    params = {
+        "size": limit,
+        "fields": ("project_id,name,primary_site,"
+                    "disease_type,summary.case_count,"
+                    "summary.file_count"),
+    }
+
+    if disease_type:
+        params["filters"] = (
+            '{"op":"=","content":{"field":'
+            f'"disease_type","value":"{disease_type}"}}}}'
+        )
+
+    resp = requests.get(url, params=params, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    rows = []
+    for hit in data.get("data", {}).get("hits", []):
+        summary = hit.get("summary", {})
+        rows.append({
+            "project_id": hit.get("project_id", ""),
+            "name": hit.get("name", ""),
+            "primary_site": "; ".join(
+                hit.get("primary_site", [])),
+            "disease_type": "; ".join(
+                hit.get("disease_type", [])),
+            "case_count": summary.get(
+                "case_count", 0),
+            "file_count": summary.get(
+                "file_count", 0),
+        })
+
+    df = pd.DataFrame(rows)
+    print(f"GDC projects: {len(df)}")
+    return df
+```
+
+## 2. ケースメタデータ
+
+```python
+def gdc_cases(project_id, limit=100):
+    """
+    GDC — ケースメタデータ取得。
+
+    Parameters:
+        project_id: str — プロジェクト ID
+            (例: "TCGA-BRCA")
+        limit: int — 最大結果数
+    """
+    url = f"{GDC_API}/cases"
+    filters = {
+        "op": "=",
+        "content": {
+            "field": "project.project_id",
+            "value": project_id,
+        },
+    }
+    params = {
+        "filters": str(filters).replace("'", '"'),
+        "fields": ("case_id,submitter_id,"
+                    "demographic.gender,"
+                    "demographic.race,"
+                    "demographic.vital_status,"
+                    "diagnoses.primary_diagnosis,"
+                    "diagnoses.tumor_stage,"
+                    "diagnoses.age_at_diagnosis"),
+        "size": limit,
+    }
+    resp = requests.get(url, params=params, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    rows = []
+    for hit in data.get("data", {}).get("hits", []):
+        demo = hit.get("demographic", {}) or {}
+        diag = (hit.get("diagnoses", [{}]) or [{}])[0]
+        rows.append({
+            "case_id": hit.get("case_id", ""),
+            "submitter_id": hit.get("submitter_id", ""),
+            "gender": demo.get("gender", ""),
+            "race": demo.get("race", ""),
+            "vital_status": demo.get(
+                "vital_status", ""),
+            "diagnosis": diag.get(
+                "primary_diagnosis", ""),
+            "stage": diag.get("tumor_stage", ""),
+            "age_at_diagnosis": diag.get(
+                "age_at_diagnosis", ""),
+        })
+
+    df = pd.DataFrame(rows)
+    print(f"GDC cases: {project_id} → {len(df)}")
+    return df
+```
+
+## 3. 体細胞変異 (SSM) 検索
+
+```python
+def gdc_ssm_by_gene(gene_symbol, project_id=None,
+                       limit=100):
+    """
+    GDC — 遺伝子別体細胞変異検索。
+
+    Parameters:
+        gene_symbol: str — 遺伝子シンボル (例: "TP53")
+        project_id: str — プロジェクト ID フィルタ
+        limit: int — 最大結果数
+    """
+    url = f"{GDC_API}/ssms"
+    filters = {
+        "op": "and",
+        "content": [
+            {
+                "op": "=",
+                "content": {
+                    "field":
+                        "consequence.transcript."
+                        "gene.symbol",
+                    "value": gene_symbol,
+                },
+            }
+        ],
+    }
+
+    if project_id:
+        filters["content"].append({
+            "op": "=",
+            "content": {
+                "field": "cases.project.project_id",
+                "value": project_id,
+            },
+        })
+
+    params = {
+        "filters": str(filters).replace("'", '"'),
+        "fields": ("ssm_id,genomic_dna_change,"
+                    "consequence.transcript.aa_change,"
+                    "consequence.transcript."
+                    "consequence_type,"
+                    "consequence.transcript."
+                    "gene.symbol"),
+        "size": limit,
+    }
+    resp = requests.get(url, params=params, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    rows = []
+    for hit in data.get("data", {}).get("hits", []):
+        for csq in hit.get("consequence", []):
+            tx = csq.get("transcript", {})
+            rows.append({
+                "ssm_id": hit.get("ssm_id", ""),
+                "genomic_change": hit.get(
+                    "genomic_dna_change", ""),
+                "gene": tx.get("gene", {}).get(
+                    "symbol", ""),
+                "aa_change": tx.get("aa_change", ""),
+                "consequence_type": tx.get(
+                    "consequence_type", ""),
+            })
+
+    df = pd.DataFrame(rows)
+    print(f"GDC SSM: {gene_symbol} → {len(df)} variants")
+    return df
+```
+
+## 4. GDC 統合パイプライン
+
+```python
+def gdc_pipeline(project_id, gene_symbol=None,
+                    output_dir="results"):
+    """
+    GDC 統合パイプライン。
+
+    Parameters:
+        project_id: str — プロジェクト ID
+        gene_symbol: str — 遺伝子フィルタ
+        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) プロジェクト情報
+    projects = gdc_projects()
+    projects.to_csv(output_dir / "gdc_projects.csv",
+                    index=False)
+
+    # 2) ケースメタデータ
+    cases = gdc_cases(project_id)
+    cases.to_csv(output_dir / "gdc_cases.csv",
+                 index=False)
+
+    # 3) 体細胞変異
+    if gene_symbol:
+        ssm = gdc_ssm_by_gene(gene_symbol, project_id)
+        ssm.to_csv(output_dir / "gdc_ssm.csv",
+                   index=False)
+
+    print(f"GDC pipeline: {project_id} → {output_dir}")
+    return {"cases": cases}
+```
+
+---
+
+## ToolUniverse 連携
+
+| TU Key | ツール名 | 連携内容 |
+|--------|---------|---------|
+| `gdc` | GDC | NCI Genomic Data Commons REST API |
+
+## パイプライン統合
+
+```
+cancer-genomics → gdc-portal → precision-oncology
+  (COSMIC/DepMap)   (GDC API)    (MTB レポート)
+        │                │              ↓
+icgc-cancer-data ───────┘    variant-interpretation
+  (ICGC DCC)                 (ClinVar/ACMG)
+```
+
+## パイプライン出力
+
+| ファイル | 説明 | 次スキル |
+|---------|------|---------|
+| `results/gdc_projects.csv` | プロジェクト一覧 | → cancer-genomics |
+| `results/gdc_cases.csv` | ケースメタデータ | → precision-oncology |
+| `results/gdc_ssm.csv` | 体細胞変異 | → variant-interpretation |