@nahisaho/satori 0.15.0 → 0.16.0

package/src/.github/skills/scientific-toxicology-env/SKILL.md

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+---
+name: scientific-toxicology-env
+description: |
+  毒性学・環境衛生スキル。CTD (Comparative Toxicogenomics Database)
+  化学-遺伝子-疾患関連・ToxCast/Tox21 高スループット毒性スクリーニング・
+  IRIS ヒトリスク評価・T3DB 食品/環境毒性物質・PubChem BioAssay 毒性データ。
+---
+
+# Scientific Toxicology & Environmental Health
+
+CTD / Tox21 / ToxCast / T3DB / IRIS を活用した毒性学・環境衛生
+パイプラインを提供する。化学物質-遺伝子-疾患関連、高スループット
+毒性スクリーニング、ヒト健康リスク評価。
+
+## When to Use
+
+- 化学物質が関連する遺伝子・疾患を調べるとき (CTD)
+- Tox21/ToxCast アッセイデータで毒性メカニズムを解析するとき
+- IRIS リスク評価データ (RfD/RfC/UR) を参照するとき
+- 食品・環境毒性物質の詳細データベース (T3DB) を検索するとき
+- PubChem BioAssay から毒性関連ハイスループットデータを取得するとき
+- ADMET 毒性予測と実験毒性データを併用するとき
+
+---
+
+## Quick Start
+
+## 1. CTD 化学-遺伝子-疾患関連検索
+
+```python
+import requests
+import pandas as pd
+import json
+
+CTD_BASE = "https://ctdbase.org/tools"
+
+
+def ctd_chemical_gene(chemical_name, limit=100):
+    """
+    CTD — 化学物質-遺伝子相互作用を検索。
+
+    Parameters:
+        chemical_name: str — 化学物質名 (例: "Bisphenol A")
+        limit: int — 最大取得数
+    """
+    url = f"{CTD_BASE}/batchQuery.go"
+    params = {
+        "inputType": "chem",
+        "inputTerms": chemical_name,
+        "report": "genes_curated",
+        "format": "json",
+    }
+    resp = requests.get(url, params=params, timeout=60)
+    resp.raise_for_status()
+    data = resp.json()[:limit]
+
+    results = []
+    for entry in data:
+        results.append({
+            "chemical": entry.get("ChemicalName", ""),
+            "gene": entry.get("GeneSymbol", ""),
+            "organism": entry.get("Organism", ""),
+            "interaction": entry.get("Interaction", ""),
+            "pubmed_ids": entry.get("PubMedIDs", ""),
+        })
+
+    df = pd.DataFrame(results)
+    print(f"CTD: {chemical_name} → {len(df)} gene interactions")
+    return df
+```
+
+## 2. CTD 化学-疾患関連検索
+
+```python
+def ctd_chemical_disease(chemical_name, limit=100):
+    """
+    CTD — 化学物質-疾患関連を検索。
+
+    Parameters:
+        chemical_name: str — 化学物質名
+        limit: int — 最大取得数
+    """
+    url = f"{CTD_BASE}/batchQuery.go"
+    params = {
+        "inputType": "chem",
+        "inputTerms": chemical_name,
+        "report": "diseases_curated",
+        "format": "json",
+    }
+    resp = requests.get(url, params=params, timeout=60)
+    resp.raise_for_status()
+    data = resp.json()[:limit]
+
+    results = []
+    for entry in data:
+        results.append({
+            "chemical": entry.get("ChemicalName", ""),
+            "disease": entry.get("DiseaseName", ""),
+            "disease_id": entry.get("DiseaseID", ""),
+            "direct_evidence": entry.get("DirectEvidence", ""),
+            "inference_score": float(entry.get("InferenceScore", 0)),
+        })
+
+    df = pd.DataFrame(results)
+    df = df.sort_values("inference_score", ascending=False)
+    print(f"CTD: {chemical_name} → {len(df)} disease associations")
+    return df
+```
+
+## 3. Tox21/ToxCast アッセイデータ取得
+
+```python
+COMPTOX_BASE = "https://comptox.epa.gov/dashboard/api"
+
+
+def tox21_assay_search(chemical_identifier, assay_source="Tox21"):
+    """
+    CompTox Dashboard — Tox21/ToxCast アッセイ結果を取得。
+
+    Parameters:
+        chemical_identifier: str — DTXSID or CAS
+        assay_source: str — "Tox21" or "ToxCast"
+    """
+    # CompTox Dashboard API で化学物質のアッセイデータ取得
+    url = f"{COMPTOX_BASE}/chemical/search"
+    params = {"query": chemical_identifier}
+    resp = requests.get(url, params=params, timeout=30)
+    resp.raise_for_status()
+    chem_data = resp.json()
+
+    dtxsid = chem_data.get("dtxsid", chemical_identifier)
+
+    # アッセイエンドポイント取得
+    url_assay = f"{COMPTOX_BASE}/chemical/{dtxsid}/assays"
+    resp_assay = requests.get(url_assay, timeout=30)
+    resp_assay.raise_for_status()
+    assays = resp_assay.json()
+
+    results = []
+    for assay in assays:
+        if assay_source.lower() in assay.get("assaySource", "").lower():
+            results.append({
+                "assay_name": assay.get("assayName", ""),
+                "assay_source": assay.get("assaySource", ""),
+                "endpoint": assay.get("assayEndpoint", ""),
+                "activity": assay.get("activity", ""),
+                "ac50_um": assay.get("ac50", None),
+                "hit_call": assay.get("hitCall", ""),
+            })
+
+    df = pd.DataFrame(results)
+    n_active = (df["hit_call"] == "Active").sum() if len(df) > 0 else 0
+    print(f"Tox21/ToxCast: {dtxsid} → {len(df)} assays, {n_active} active")
+    return df
+```
+
+## 4. T3DB 毒性物質検索
+
+```python
+T3DB_BASE = "https://t3db.ca/api"
+
+
+def t3db_search(query, search_type="name"):
+    """
+    T3DB — 食品/環境毒性物質データベース検索。
+
+    Parameters:
+        query: str — 検索語
+        search_type: str — "name", "cas", "category"
+    """
+    url = f"{T3DB_BASE}/toxins/search"
+    params = {"query": query, "search_type": search_type}
+    resp = requests.get(url, params=params, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    results = []
+    for toxin in data.get("toxins", []):
+        results.append({
+            "name": toxin.get("name", ""),
+            "t3db_id": toxin.get("t3db_id", ""),
+            "cas_number": toxin.get("cas_number", ""),
+            "category": toxin.get("category", ""),
+            "toxicity_class": toxin.get("toxicity_class", ""),
+            "ld50_oral": toxin.get("ld50_oral", ""),
+            "target_organs": toxin.get("target_organs", []),
+        })
+
+    df = pd.DataFrame(results)
+    print(f"T3DB: '{query}' → {len(df)} toxins")
+    return df
+```
+
+## 5. EPA IRIS リスク評価
+
+```python
+def iris_risk_assessment(chemical_name):
+    """
+    EPA IRIS — ヒト健康リスク評価データ取得。
+
+    Parameters:
+        chemical_name: str — 化学物質名
+    """
+    url = "https://iris.epa.gov/AtoZ"
+    resp = requests.get(url, timeout=30)
+
+    # IRIS は構造化 API なし — スクレイピングまたはローカルデータ
+    # 代替: CompTox Dashboard API 経由
+    url_comptox = f"{COMPTOX_BASE}/chemical/search"
+    params = {"query": chemical_name}
+    resp = requests.get(url_comptox, params=params, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    risk_data = {
+        "chemical": chemical_name,
+        "dtxsid": data.get("dtxsid", ""),
+        "rfd_oral_mg_kg_day": data.get("rfdOral", None),
+        "rfc_inhalation_mg_m3": data.get("rfcInhalation", None),
+        "cancer_classification": data.get("cancerClassification", ""),
+        "oral_slope_factor": data.get("oralSlopeFactor", None),
+        "inhalation_unit_risk": data.get("inhalationUnitRisk", None),
+    }
+
+    print(f"IRIS: {chemical_name}")
+    for k, v in risk_data.items():
+        if v and k != "chemical":
+            print(f"  {k}: {v}")
+    return risk_data
+```
+
+## 6. 毒性パスウェイ解析
+
+```python
+def toxicity_pathway_analysis(chemical_name, species="Homo sapiens"):
+    """
+    CTD + パスウェイ統合毒性解析。
+
+    Parameters:
+        chemical_name: str — 化学物質名
+        species: str — 生物種
+    """
+    # 1) CTD 遺伝子取得
+    gene_df = ctd_chemical_gene(chemical_name, limit=500)
+    if species:
+        gene_df = gene_df[gene_df["organism"] == species]
+
+    gene_list = gene_df["gene"].unique().tolist()
+
+    # 2) CTD 疾患取得
+    disease_df = ctd_chemical_disease(chemical_name, limit=100)
+
+    # 3) パスウェイ濃縮 (KEGG enrichment via Enrichr)
+    enrichr_url = "https://maayanlab.cloud/Enrichr"
+    add_resp = requests.post(
+        f"{enrichr_url}/addList",
+        files={"list": (None, "\n".join(gene_list))}
+    )
+    user_list_id = add_resp.json()["userListId"]
+
+    enrich_resp = requests.get(
+        f"{enrichr_url}/enrich",
+        params={"userListId": user_list_id, "backgroundType": "KEGG_2021_Human"}
+    )
+    pathways = enrich_resp.json().get("KEGG_2021_Human", [])
+
+    pathway_results = []
+    for pw in pathways[:20]:
+        pathway_results.append({
+            "pathway": pw[1],
+            "p_value": pw[2],
+            "adj_p_value": pw[6],
+            "genes": pw[5],
+        })
+
+    print(f"Toxicity pathway: {chemical_name}")
+    print(f"  Target genes: {len(gene_list)}")
+    print(f"  Diseases: {len(disease_df)}")
+    print(f"  Pathways: {len(pathway_results)}")
+    return {
+        "genes": gene_df,
+        "diseases": disease_df,
+        "pathways": pd.DataFrame(pathway_results),
+    }
+```
+
+---
+
+## パイプライン統合
+
+```
+admet-pharmacokinetics → toxicology-env → pharmacovigilance
+  (ADMET 毒性予測)       (CTD/Tox21/IRIS)   (市販後安全性)
+        │                       │                  ↓
+cheminformatics ───────────────┘           disease-research
+  (RDKit 構造アラート)    │                (疾患-遺伝子関連)
+                          ↓
+                   public-health-data
+                   (CDC/WHO 公衆衛生)
+```
+
+## パイプライン出力
+
+| ファイル | 説明 | 次スキル |
+|---------|------|---------|
+| `results/ctd_gene_interactions.csv` | CTD 化学-遺伝子関連 | → pathway-enrichment |
+| `results/ctd_disease_associations.csv` | CTD 化学-疾患関連 | → disease-research |
+| `results/tox21_assays.csv` | Tox21/ToxCast アッセイ結果 | → admet-pharmacokinetics |
+| `results/toxicity_pathways.json` | 毒性パスウェイ解析結果 | → pharmacovigilance |