@nahisaho/satori 0.17.0 → 0.19.0

package/src/.github/skills/scientific-reactome-pathways/SKILL.md

@@ -0,0 +1,242 @@
+---
+name: scientific-reactome-pathways
+description: |
+  Reactome パスウェイスキル。Reactome Content Service
+  REST API によるパスウェイ検索・階層取得・UniProt マッピング・
+  パスウェイ図データ取得。ToolUniverse 連携: reactome。
+tu_tools:
+  - key: reactome
+    name: Reactome
+    description: パスウェイデータベース REST API
+---
+
+# Scientific Reactome Pathways
+
+Reactome Content Service REST API を活用したパスウェイ検索・
+階層構造取得・UniProt アクセッション→パスウェイマッピング・
+パスウェイ図データ取得パイプラインを提供する。
+
+## When to Use
+
+- 生物学パスウェイを名前やキーワードで検索するとき
+- パスウェイ階層ツリーを取得するとき
+- UniProt アクセッションからパスウェイをマッピングするとき
+- パスウェイの参加者 (タンパク質/化合物) を列挙するとき
+- パスウェイ図のレイアウトデータを取得するとき
+
+---
+
+## Quick Start
+
+## 1. パスウェイ検索・詳細取得
+
+```python
+import requests
+import pandas as pd
+
+REACTOME = "https://reactome.org/ContentService"
+
+
+def reactome_search(query, species="Homo sapiens",
+                       limit=25):
+    """
+    Reactome — パスウェイ検索。
+
+    Parameters:
+        query: str — 検索クエリ (例: "apoptosis", "MAPK")
+        species: str — 種名 (例: "Homo sapiens")
+        limit: int — 最大結果数
+    """
+    url = f"{REACTOME}/search/query"
+    params = {
+        "query": query,
+        "species": species,
+        "types": "Pathway",
+        "cluster": "true",
+    }
+    resp = requests.get(url, params=params, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    rows = []
+    for group in data.get("results", []):
+        for entry in group.get("entries", [])[:limit]:
+            rows.append({
+                "stId": entry.get("stId", ""),
+                "name": entry.get("name", ""),
+                "species": entry.get("species", ""),
+                "exact_type": entry.get(
+                    "exactType", ""),
+                "compartments": "; ".join(
+                    entry.get("compartmentNames", [])),
+            })
+
+    df = pd.DataFrame(rows[:limit])
+    print(f"Reactome search: '{query}' → {len(df)} "
+          f"pathways")
+    return df
+
+
+def reactome_pathway_detail(pathway_id):
+    """
+    Reactome — パスウェイ詳細取得。
+
+    Parameters:
+        pathway_id: str — Reactome Stable ID
+            (例: "R-HSA-109581")
+    """
+    url = f"{REACTOME}/data/pathway/{pathway_id}"
+    resp = requests.get(url, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    result = {
+        "stId": data.get("stId", ""),
+        "name": data.get("displayName", ""),
+        "species": data.get("speciesName", ""),
+        "is_inferred": data.get("isInferred", False),
+        "has_diagram": data.get("hasDiagram", False),
+        "n_sub_events": len(
+            data.get("hasEvent", [])),
+        "n_compartments": len(
+            data.get("compartment", [])),
+        "release_date": data.get("releaseDate", ""),
+    }
+    return result
+```
+
+## 2. UniProt→パスウェイ マッピング
+
+```python
+def reactome_uniprot_pathways(uniprot_id,
+                                  species="Homo sapiens"):
+    """
+    Reactome — UniProt → パスウェイマッピング。
+
+    Parameters:
+        uniprot_id: str — UniProt アクセッション
+            (例: "P38398" = BRCA1)
+        species: str — 種名
+    """
+    url = f"{REACTOME}/data/pathways/low/entity/{uniprot_id}"
+    params = {"species": species}
+    resp = requests.get(url, params=params, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    rows = []
+    for pw in data:
+        rows.append({
+            "pathway_id": pw.get("stId", ""),
+            "pathway_name": pw.get("displayName", ""),
+            "species": pw.get("speciesName", ""),
+            "has_diagram": pw.get("hasDiagram", False),
+        })
+
+    df = pd.DataFrame(rows)
+    print(f"Reactome UniProt→pathway: {uniprot_id} "
+          f"→ {len(df)} pathways")
+    return df
+```
+
+## 3. パスウェイ参加者取得
+
+```python
+def reactome_participants(pathway_id):
+    """
+    Reactome — パスウェイ参加者一覧。
+
+    Parameters:
+        pathway_id: str — Reactome Stable ID
+    """
+    url = (f"{REACTOME}/data/participants/"
+           f"{pathway_id}")
+    resp = requests.get(url, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    rows = []
+    for item in data:
+        pe_name = item.get("displayName", "")
+        for ref in item.get("refEntities", []):
+            rows.append({
+                "pathway_id": pathway_id,
+                "participant": pe_name,
+                "db_name": ref.get("databaseName", ""),
+                "identifier": ref.get("identifier", ""),
+                "name": ref.get("displayName", ""),
+            })
+
+    df = pd.DataFrame(rows)
+    print(f"Reactome participants: {pathway_id} "
+          f"→ {len(df)} entities")
+    return df
+```
+
+## 4. Reactome 統合パイプライン
+
+```python
+def reactome_pipeline(query_or_uniprot,
+                         output_dir="results"):
+    """
+    Reactome 統合パイプライン。
+
+    Parameters:
+        query_or_uniprot: str — 検索クエリ or UniProt ID
+        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)
+
+    is_uniprot = (len(query_or_uniprot) == 6
+                  and query_or_uniprot[0].isalpha())
+
+    if is_uniprot:
+        # UniProt → パスウェイ
+        pathways = reactome_uniprot_pathways(
+            query_or_uniprot)
+    else:
+        # テキスト検索
+        pathways = reactome_search(query_or_uniprot)
+
+    pathways.to_csv(output_dir / "reactome_pathways.csv",
+                    index=False)
+
+    # トップパスウェイの参加者
+    if not pathways.empty:
+        top_id = (pathways.iloc[0].get("pathway_id")
+                  or pathways.iloc[0].get("stId"))
+        parts = reactome_participants(top_id)
+        parts.to_csv(
+            output_dir / "reactome_participants.csv",
+            index=False)
+
+    print(f"Reactome pipeline: {output_dir}")
+    return {"pathways": pathways}
+```
+
+---
+
+## ToolUniverse 連携
+
+| TU Key | ツール名 | 連携内容 |
+|--------|---------|---------|
+| `reactome` | Reactome | パスウェイデータベース REST API |
+
+## パイプライン統合
+
+```
+pathway-enrichment → reactome-pathways → systems-biology
+  (GO/パスウェイ)     (Reactome API)     (ネットワーク解析)
+        │                   │                 ↓
+uniprot-proteome ──────────┘       metabolomics-databases
+  (UniProt ID)                     (MetaCyc 代謝)
+```
+
+## パイプライン出力
+
+| ファイル | 説明 | 次スキル |
+|---------|------|---------|
+| `results/reactome_pathways.csv` | パスウェイ一覧 | → pathway-enrichment |
+| `results/reactome_participants.csv` | 参加者 | → protein-interaction-network |

package/src/.github/skills/scientific-semantic-scholar/SKILL.md

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+---
+name: scientific-semantic-scholar
+description: |
+  Semantic Scholar 学術グラフスキル。Semantic Scholar Academic
+  Graph API による論文検索・著者プロファイル・引用グラフ・
+  推薦・TLDR 要約。ToolUniverse 連携: semantic_scholar。
+tu_tools:
+  - key: semantic_scholar
+    name: Semantic Scholar
+    description: 学術論文検索・引用解析・著者プロファイル
+---
+
+# Scientific Semantic Scholar
+
+Semantic Scholar Academic Graph API を活用した学術論文検索・
+引用ネットワーク解析・著者プロファイル・論文推薦パイプライン
+を提供する。
+
+## When to Use
+
+- 学術論文を高精度で検索するとき
+- 引用・被引用ネットワークを解析するとき
+- 著者の h-index・論文数・研究領域を調べるとき
+- 関連論文の推薦を受けるとき
+- TLDR (自動要約) を取得するとき
+- 特定分野の引用傾向を分析するとき
+- PubMed/OpenAlex 以外の学術検索エンジンを使うとき
+
+---
+
+## Quick Start
+
+## 1. 論文検索
+
+```python
+import requests
+import pandas as pd
+
+S2_BASE = "https://api.semanticscholar.org/graph/v1"
+S2_HEADERS = {}  # API key: {"x-api-key": "YOUR_KEY"}
+
+
+def semantic_scholar_search(query, limit=50,
+                              year_range=None,
+                              fields_of_study=None):
+    """
+    Semantic Scholar — 論文検索。
+
+    Parameters:
+        query: str — 検索クエリ
+        limit: int — 最大結果数
+        year_range: str — 年範囲 (例: "2020-2024")
+        fields_of_study: list[str] — 分野フィルタ
+    """
+    url = f"{S2_BASE}/paper/search"
+    params = {
+        "query": query,
+        "limit": min(limit, 100),
+        "fields": ("paperId,title,year,citationCount,"
+                    "influentialCitationCount,authors,"
+                    "journal,tldr,openAccessPdf,fieldsOfStudy"),
+    }
+    if year_range:
+        params["year"] = year_range
+    if fields_of_study:
+        params["fieldsOfStudy"] = ",".join(fields_of_study)
+
+    resp = requests.get(url, params=params,
+                        headers=S2_HEADERS, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    results = []
+    for p in data.get("data", []):
+        authors = [a.get("name", "") for a in p.get("authors", [])]
+        tldr_text = ""
+        if p.get("tldr"):
+            tldr_text = p["tldr"].get("text", "")
+        results.append({
+            "paper_id": p.get("paperId", ""),
+            "title": p.get("title", ""),
+            "year": p.get("year"),
+            "citation_count": p.get("citationCount", 0),
+            "influential_citations": p.get(
+                "influentialCitationCount", 0),
+            "authors": "; ".join(authors[:5]),
+            "journal": (p.get("journal") or {}).get("name", ""),
+            "fields": ", ".join(p.get("fieldsOfStudy") or []),
+            "tldr": tldr_text[:300],
+            "pdf_url": (p.get("openAccessPdf") or {}).get("url", ""),
+        })
+
+    df = pd.DataFrame(results)
+    print(f"Semantic Scholar: {len(df)} papers "
+          f"(query='{query}')")
+    return df
+
+
+def semantic_scholar_get_paper(paper_id):
+    """
+    Semantic Scholar — 論文詳細取得。
+
+    Parameters:
+        paper_id: str — S2 Paper ID / DOI / ArXiv ID
+    """
+    url = f"{S2_BASE}/paper/{paper_id}"
+    params = {
+        "fields": ("paperId,title,year,abstract,citationCount,"
+                    "influentialCitationCount,authors,references,"
+                    "citations,journal,tldr,openAccessPdf,"
+                    "fieldsOfStudy,publicationDate,venue"),
+    }
+    resp = requests.get(url, params=params,
+                        headers=S2_HEADERS, timeout=30)
+    resp.raise_for_status()
+    return resp.json()
+```
+
+## 2. 著者プロファイル・引用解析
+
+```python
+def semantic_scholar_author(author_id, paper_limit=100):
+    """
+    Semantic Scholar — 著者プロファイル取得。
+
+    Parameters:
+        author_id: str — S2 Author ID
+        paper_limit: int — 取得論文数上限
+    """
+    url = f"{S2_BASE}/author/{author_id}"
+    params = {
+        "fields": ("authorId,name,affiliations,homepage,"
+                    "paperCount,citationCount,hIndex"),
+    }
+    resp = requests.get(url, params=params,
+                        headers=S2_HEADERS, timeout=30)
+    resp.raise_for_status()
+    profile = resp.json()
+
+    # 論文一覧
+    papers_url = f"{S2_BASE}/author/{author_id}/papers"
+    p_params = {
+        "fields": "paperId,title,year,citationCount,venue",
+        "limit": min(paper_limit, 1000),
+    }
+    p_resp = requests.get(papers_url, params=p_params,
+                          headers=S2_HEADERS, timeout=30)
+    p_resp.raise_for_status()
+
+    papers = []
+    for p in p_resp.json().get("data", []):
+        papers.append({
+            "paper_id": p.get("paperId", ""),
+            "title": p.get("title", ""),
+            "year": p.get("year"),
+            "citations": p.get("citationCount", 0),
+            "venue": p.get("venue", ""),
+        })
+
+    papers_df = pd.DataFrame(papers)
+
+    print(f"Author {profile.get('name', '')}: "
+          f"h-index={profile.get('hIndex', 0)}, "
+          f"{profile.get('paperCount', 0)} papers, "
+          f"{profile.get('citationCount', 0)} citations")
+    return profile, papers_df
+```
+
+## 3. 引用ネットワーク・影響度分析
+
+```python
+def semantic_scholar_citation_graph(paper_id,
+                                       direction="both",
+                                       limit=100):
+    """
+    Semantic Scholar — 引用グラフ取得。
+
+    Parameters:
+        paper_id: str — S2 Paper ID
+        direction: str — "citations", "references", "both"
+        limit: int — 各方向の上限
+    """
+    graphs = {}
+    fields = "paperId,title,year,citationCount,authors"
+
+    if direction in ("citations", "both"):
+        url = f"{S2_BASE}/paper/{paper_id}/citations"
+        resp = requests.get(url, params={"fields": fields,
+                            "limit": limit},
+                            headers=S2_HEADERS, timeout=30)
+        resp.raise_for_status()
+        cites = []
+        for c in resp.json().get("data", []):
+            cp = c.get("citingPaper", {})
+            cites.append({
+                "paper_id": cp.get("paperId", ""),
+                "title": cp.get("title", ""),
+                "year": cp.get("year"),
+                "citations": cp.get("citationCount", 0),
+            })
+        graphs["citations"] = pd.DataFrame(cites)
+
+    if direction in ("references", "both"):
+        url = f"{S2_BASE}/paper/{paper_id}/references"
+        resp = requests.get(url, params={"fields": fields,
+                            "limit": limit},
+                            headers=S2_HEADERS, timeout=30)
+        resp.raise_for_status()
+        refs = []
+        for r in resp.json().get("data", []):
+            rp = r.get("citedPaper", {})
+            refs.append({
+                "paper_id": rp.get("paperId", ""),
+                "title": rp.get("title", ""),
+                "year": rp.get("year"),
+                "citations": rp.get("citationCount", 0),
+            })
+        graphs["references"] = pd.DataFrame(refs)
+
+    for k, v in graphs.items():
+        print(f"  {k}: {len(v)} papers")
+    return graphs
+```
+
+## 4. 学術文献統合パイプライン
+
+```python
+def semantic_scholar_pipeline(query, year_range=None,
+                                 output_dir="results"):
+    """
+    Semantic Scholar 統合パイプライン。
+
+    Parameters:
+        query: str — 検索クエリ
+        year_range: str — 年範囲
+        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) 論文検索
+    papers = semantic_scholar_search(query,
+                                     year_range=year_range)
+    papers.to_csv(output_dir / "papers.csv", index=False)
+
+    # 2) トップ被引用論文の引用グラフ
+    if not papers.empty:
+        top = papers.sort_values("citation_count",
+                                  ascending=False).iloc[0]
+        pid = top["paper_id"]
+        graphs = semantic_scholar_citation_graph(pid)
+        for k, df in graphs.items():
+            df.to_csv(output_dir / f"{k}.csv", index=False)
+
+    # 3) 年次引用傾向
+    if not papers.empty and "year" in papers.columns:
+        yearly = papers.groupby("year").agg(
+            papers_count=("paper_id", "count"),
+            total_citations=("citation_count", "sum"),
+            avg_citations=("citation_count", "mean"),
+        ).reset_index()
+        yearly.to_csv(output_dir / "yearly_trend.csv",
+                      index=False)
+
+    print(f"Semantic Scholar pipeline: {output_dir}")
+    return {"papers": papers}
+```
+
+---
+
+## ToolUniverse 連携
+
+| TU Key | ツール名 | 連携内容 |
+|--------|---------|---------|
+| `semantic_scholar` | Semantic Scholar | 論文検索・引用解析・著者・TLDR |
+
+## パイプライン統合
+
+```
+literature-search → semantic-scholar → deep-research
+  (PubMed/NCBI)   (Academic Graph API) (knowledge synthesis)
+       │                  │                    ↓
+  crossref-metadata ─────┘             citation-checker
+  (DOI/metadata)     │                 (引用品質検証)
+                     ↓
+            gene-expression-transcriptomics
+            (論文引用データからの解析)
+```
+
+## パイプライン出力
+
+| ファイル | 説明 | 次スキル |
+|---------|------|---------|
+| `results/papers.csv` | 論文検索結果 | → deep-research |
+| `results/citations.csv` | 被引用論文 | → citation-checker |
+| `results/references.csv` | 引用論文 | → meta-analysis |
+| `results/yearly_trend.csv` | 年次引用傾向 | → bibliometrics |