@nahisaho/satori 0.11.0 → 0.12.0

package/src/.github/skills/scientific-literature-search/SKILL.md

@@ -0,0 +1,443 @@
+---
+name: scientific-literature-search
+description: |
+  学術文献検索・取得スキル。PubMed E-utilities、Semantic Scholar、
+  OpenAlex、EuropePMC、CrossRef の 5 大学術データベース API を統合した
+  文献検索パイプライン。MeSH 構造化検索、引用ネットワーク分析、
+  著者/機関メトリクス、全文取得、PICO ベース検索戦略対応。
+  29 の ToolUniverse SMCP ツールと連携。
+---
+
+# Scientific Literature Search
+
+PubMed / Semantic Scholar / OpenAlex / EuropePMC / CrossRef の
+5 大学術 DB を統合した文献検索・メタデータ取得パイプラインを提供する。
+
+## When to Use
+
+- PubMed で MeSH 用語を用いた構造化検索が必要なとき
+- Semantic Scholar でセマンティック類似論文を発見するとき
+- OpenAlex で著者・機関・ジャーナルメトリクスを分析するとき
+- 特定論文の引用/被引用ネットワークを構築するとき
+- 系統的レビューのためのマルチ DB 横断検索が必要なとき
+
+---
+
+## Quick Start
+
+## 1. PubMed E-utilities 検索
+
+```python
+import requests
+import xml.etree.ElementTree as ET
+import pandas as pd
+import time
+
+
+def pubmed_search(query, max_results=100, sort="relevance",
+                  date_from=None, date_to=None, rettype="xml"):
+    """
+    PubMed E-utilities による構造化検索。
+
+    Parameters:
+        query: str — PubMed クエリ (MeSH 構文対応)
+        max_results: int — 最大取得件数
+        sort: "relevance" or "date"
+        date_from/to: "YYYY/MM/DD" フォーマット
+    """
+    base = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils"
+
+    # Step 1: esearch — PMID 取得
+    params = {
+        "db": "pubmed",
+        "term": query,
+        "retmax": max_results,
+        "sort": sort,
+        "retmode": "json",
+    }
+    if date_from:
+        params["mindate"] = date_from
+        params["datetype"] = "pdat"
+    if date_to:
+        params["maxdate"] = date_to
+
+    resp = requests.get(f"{base}/esearch.fcgi", params=params)
+    data = resp.json()
+    pmids = data["esearchresult"]["idlist"]
+    total = int(data["esearchresult"]["count"])
+    print(f"PubMed search: {total} total results, fetching {len(pmids)}")
+
+    if not pmids:
+        return pd.DataFrame()
+
+    # Step 2: efetch — 詳細取得
+    time.sleep(0.4)
+    fetch_params = {
+        "db": "pubmed",
+        "id": ",".join(pmids),
+        "rettype": "xml",
+        "retmode": "xml",
+    }
+    resp = requests.get(f"{base}/efetch.fcgi", params=fetch_params)
+    root = ET.fromstring(resp.text)
+
+    articles = []
+    for article in root.findall(".//PubmedArticle"):
+        medline = article.find(".//MedlineCitation")
+        pmid = medline.findtext("PMID", "")
+        title = medline.findtext(".//ArticleTitle", "")
+        abstract = medline.findtext(".//AbstractText", "")
+        journal = medline.findtext(".//Journal/Title", "")
+        year = medline.findtext(".//PubDate/Year", "")
+
+        authors = []
+        for author in medline.findall(".//Author"):
+            last = author.findtext("LastName", "")
+            fore = author.findtext("ForeName", "")
+            if last:
+                authors.append(f"{last} {fore}")
+
+        mesh_terms = [m.findtext("DescriptorName", "")
+                      for m in medline.findall(".//MeshHeading")]
+
+        articles.append({
+            "pmid": pmid,
+            "title": title,
+            "abstract": abstract[:500],
+            "journal": journal,
+            "year": year,
+            "authors": "; ".join(authors[:5]),
+            "mesh_terms": "; ".join(mesh_terms[:10]),
+        })
+
+    return pd.DataFrame(articles)
+```
+
+## 2. Semantic Scholar API 検索
+
+```python
+def semantic_scholar_search(query, max_results=50, year_from=None,
+                             fields=None):
+    """
+    Semantic Scholar Academic Graph API 検索。
+
+    Parameters:
+        query: str — 検索クエリ
+        fields: list — 取得フィールド
+    """
+    url = "https://api.semanticscholar.org/graph/v1/paper/search"
+
+    if fields is None:
+        fields = ["title", "abstract", "year", "citationCount",
+                  "influentialCitationCount", "authors", "url",
+                  "openAccessPdf"]
+
+    params = {
+        "query": query,
+        "limit": min(max_results, 100),
+        "fields": ",".join(fields),
+    }
+    if year_from:
+        params["year"] = f"{year_from}-"
+
+    resp = requests.get(url, params=params)
+    data = resp.json()
+    papers = data.get("data", [])
+
+    results = []
+    for p in papers:
+        results.append({
+            "paper_id": p.get("paperId", ""),
+            "title": p.get("title", ""),
+            "abstract": (p.get("abstract") or "")[:300],
+            "year": p.get("year"),
+            "citations": p.get("citationCount", 0),
+            "influential_citations": p.get("influentialCitationCount", 0),
+            "authors": "; ".join([a.get("name", "")
+                                  for a in (p.get("authors") or [])[:5]]),
+            "url": p.get("url", ""),
+            "open_access": bool(p.get("openAccessPdf")),
+        })
+
+    df = pd.DataFrame(results)
+    print(f"Semantic Scholar: {data.get('total', 0)} total, "
+          f"{len(df)} fetched")
+    return df
+```
+
+## 3. OpenAlex 著者・機関メトリクス
+
+```python
+def openalex_search(query, entity_type="works", max_results=50,
+                     filters=None):
+    """
+    OpenAlex API 検索 (250M+ works, 90M+ authors)。
+
+    Parameters:
+        query: str — 検索クエリ
+        entity_type: "works", "authors", "institutions", "concepts"
+        filters: dict — OpenAlex フィルタ (e.g., {"from_publication_date": "2020-01-01"})
+    """
+    base = "https://api.openalex.org"
+    url = f"{base}/{entity_type}"
+
+    params = {
+        "search": query,
+        "per-page": min(max_results, 200),
+        "mailto": "research@example.com",
+    }
+    if filters:
+        filter_parts = [f"{k}:{v}" for k, v in filters.items()]
+        params["filter"] = ",".join(filter_parts)
+
+    resp = requests.get(url, params=params)
+    data = resp.json()
+
+    results = data.get("results", [])
+    total = data.get("meta", {}).get("count", 0)
+    print(f"OpenAlex {entity_type}: {total} total, {len(results)} fetched")
+
+    if entity_type == "works":
+        return pd.DataFrame([{
+            "id": r.get("id", ""),
+            "title": r.get("title", ""),
+            "year": r.get("publication_year"),
+            "citations": r.get("cited_by_count", 0),
+            "doi": r.get("doi", ""),
+            "type": r.get("type", ""),
+            "open_access": r.get("open_access", {}).get("is_oa", False),
+        } for r in results])
+    elif entity_type == "authors":
+        return pd.DataFrame([{
+            "id": r.get("id", ""),
+            "name": r.get("display_name", ""),
+            "works_count": r.get("works_count", 0),
+            "citations": r.get("cited_by_count", 0),
+            "h_index": r.get("summary_stats", {}).get("h_index", 0),
+            "institution": (r.get("last_known_institutions") or [{}])[0].get(
+                "display_name", "") if r.get("last_known_institutions") else "",
+        } for r in results])
+
+    return results
+```
+
+## 4. EuropePMC 全文検索
+
+```python
+def europepmc_search(query, max_results=50, source="MED",
+                      open_access_only=False):
+    """
+    EuropePMC REST API 検索 (39M+ records)。
+
+    Parameters:
+        query: str — 検索クエリ
+        source: "MED" (PubMed), "PMC" (PubMed Central), "AGR", "CBA"
+        open_access_only: True でオープンアクセスのみ
+    """
+    url = "https://www.ebi.ac.uk/europepmc/webservices/rest/search"
+
+    q = query
+    if open_access_only:
+        q += " AND OPEN_ACCESS:y"
+
+    params = {
+        "query": q,
+        "resultType": "core",
+        "pageSize": min(max_results, 100),
+        "format": "json",
+        "src": source,
+    }
+
+    resp = requests.get(url, params=params)
+    data = resp.json()
+    results = data.get("resultList", {}).get("result", [])
+    total = data.get("hitCount", 0)
+
+    articles = []
+    for r in results:
+        articles.append({
+            "pmid": r.get("pmid", ""),
+            "pmcid": r.get("pmcid", ""),
+            "title": r.get("title", ""),
+            "journal": r.get("journalTitle", ""),
+            "year": r.get("pubYear", ""),
+            "citations": r.get("citedByCount", 0),
+            "has_fulltext": r.get("hasTextMinedTerms", "N") == "Y",
+            "is_open_access": r.get("isOpenAccess", "N") == "Y",
+        })
+
+    df = pd.DataFrame(articles)
+    print(f"EuropePMC: {total} total, {len(df)} fetched")
+    return df
+```
+
+## 5. CrossRef メタデータ取得
+
+```python
+def crossref_search(query, max_results=50, filter_type=None,
+                     from_date=None, sort="relevance"):
+    """
+    CrossRef REST API 検索 (DOI メタデータ)。
+
+    Parameters:
+        query: str — 検索クエリ
+        filter_type: str — DOI タイプフィルタ ("journal-article", "book-chapter")
+        from_date: str — "YYYY-MM-DD"
+        sort: "relevance", "published", "is-referenced-by-count"
+    """
+    url = "https://api.crossref.org/works"
+    params = {
+        "query": query,
+        "rows": min(max_results, 100),
+        "sort": sort,
+        "mailto": "research@example.com",
+    }
+
+    filters = []
+    if filter_type:
+        filters.append(f"type:{filter_type}")
+    if from_date:
+        filters.append(f"from-pub-date:{from_date}")
+    if filters:
+        params["filter"] = ",".join(filters)
+
+    resp = requests.get(url, params=params)
+    data = resp.json()
+    items = data.get("message", {}).get("items", [])
+    total = data.get("message", {}).get("total-results", 0)
+
+    results = []
+    for item in items:
+        title = item.get("title", [""])[0] if item.get("title") else ""
+        results.append({
+            "doi": item.get("DOI", ""),
+            "title": title,
+            "journal": item.get("container-title", [""])[0] if item.get("container-title") else "",
+            "year": item.get("published", {}).get("date-parts", [[None]])[0][0],
+            "citations": item.get("is-referenced-by-count", 0),
+            "type": item.get("type", ""),
+            "publisher": item.get("publisher", ""),
+        })
+
+    df = pd.DataFrame(results)
+    print(f"CrossRef: {total} total, {len(df)} fetched")
+    return df
+```
+
+## 6. 引用ネットワーク構築
+
+```python
+def build_citation_network(seed_pmids, depth=1, max_per_level=20):
+    """
+    PubMed 論文の引用/被引用ネットワーク構築。
+
+    Parameters:
+        seed_pmids: list — 起点となる PMID リスト
+        depth: int — 探索深度 (1=直接引用のみ)
+        max_per_level: int — 各レベルの最大ノード数
+    """
+    import networkx as nx
+
+    G = nx.DiGraph()
+    visited = set()
+    current_level = set(seed_pmids)
+
+    for level in range(depth + 1):
+        next_level = set()
+        for pmid in list(current_level)[:max_per_level]:
+            if pmid in visited:
+                continue
+            visited.add(pmid)
+            G.add_node(pmid, level=level, is_seed=(level == 0))
+
+            # elink で引用関係取得
+            time.sleep(0.4)
+            url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi"
+            params = {
+                "dbfrom": "pubmed", "db": "pubmed",
+                "id": pmid, "linkname": "pubmed_pubmed_citedin",
+                "retmode": "json",
+            }
+            try:
+                resp = requests.get(url, params=params)
+                data = resp.json()
+                links = data.get("linksets", [{}])[0].get("linksetdbs", [])
+                if links:
+                    cited_by = [l["id"] for l in links[0].get("links", [])[:max_per_level]]
+                    for citing in cited_by:
+                        G.add_edge(citing, pmid)
+                        next_level.add(citing)
+            except Exception:
+                continue
+
+        current_level = next_level - visited
+
+    print(f"Citation network: {G.number_of_nodes()} nodes, "
+          f"{G.number_of_edges()} edges, depth={depth}")
+    return G
+```
+
+## References
+
+### Output Files
+
+| ファイル | 形式 |
+|---|---|
+| `results/pubmed_search.csv` | CSV |
+| `results/semantic_scholar_results.csv` | CSV |
+| `results/openalex_results.csv` | CSV |
+| `results/europepmc_results.csv` | CSV |
+| `results/crossref_results.csv` | CSV |
+| `results/citation_network.graphml` | GraphML |
+| `figures/citation_network.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 |
+|---|---|---|
+| PubMed | `PubMed_search_articles` | PubMed 論文検索 |
+| PubMed | `PubMed_get_article` | 論文詳細取得 |
+| PubMed | `PubMed_get_cited_by` | 被引用論文取得 |
+| PubMed | `PubMed_get_related` | 関連論文検索 |
+| PubMed | `PubMed_get_links` | 関連リンク取得 |
+| PubMed | `PubMed_Guidelines_Search` | ガイドライン検索 |
+| EuropePMC | `EuropePMC_search_articles` | EuropePMC 検索 |
+| EuropePMC | `EuropePMC_get_article` | 記事詳細取得 |
+| EuropePMC | `EuropePMC_get_references` | 参考文献取得 |
+| EuropePMC | `EuropePMC_get_citations` | 引用取得 |
+| EuropePMC | `EuropePMC_get_fulltext` | 全文取得 |
+| EuropePMC | `EuropePMC_get_fulltext_snippets` | 全文スニペット |
+| EuropePMC | `EuropePMC_Guidelines_Search` | ガイドライン検索 |
+| Semantic Scholar | `SemanticScholar_search_papers` | セマンティック論文検索 |
+| Semantic Scholar | `SemanticScholar_get_pdf_snippets` | PDF スニペット |
+| OpenAlex | `openalex_literature_search` | 文献検索 |
+| OpenAlex | `openalex_get_work` | 論文詳細 |
+| OpenAlex | `openalex_get_work_by_doi` | DOI → 論文 |
+| OpenAlex | `openalex_search_works` | 論文検索 (REST) |
+| OpenAlex | `openalex_get_author` | 著者詳細 |
+| OpenAlex | `openalex_search_authors` | 著者検索 |
+| OpenAlex | `openalex_get_institution` | 機関詳細 |
+| OpenAlex | `openalex_search_institutions` | 機関検索 |
+| CrossRef | `Crossref_search_works` | DOI メタデータ検索 |
+| CrossRef | `Crossref_get_work` | 論文メタデータ取得 |
+| CrossRef | `Crossref_get_funder` | 助成機関情報 |
+| CrossRef | `Crossref_get_journal` | ジャーナル情報 |
+| CrossRef | `Crossref_list_funders` | 助成機関一覧 |
+| CrossRef | `Crossref_list_types` | 出版タイプ一覧 |
+
+### 参照スキル
+
+| スキル | 関連 |
+|---|---|
+| `scientific-deep-research` | 文献検索 → 深層リサーチ |
+| `scientific-citation-checker` | 引用検証連携 |
+| `scientific-systematic-review` | 系統的検索戦略 |
+| `scientific-meta-analysis` | メタアナリシス文献収集 |
+| `scientific-academic-writing` | 関連文献の自動発見 |
+| `scientific-text-mining-nlp` | 抽出テキストの NLP 解析 |
+
+### 依存パッケージ
+
+`requests`, `pandas`, `networkx`, `xml.etree.ElementTree` (stdlib)

package/src/.github/skills/scientific-meta-analysis/SKILL.md

@@ -355,6 +355,16 @@ def cumulative_meta_analysis(studies_df, sort_by="year", model="random"):
 | EuropePMC | `EuropePMC_search_articles` | ヨーロッパ文献検索 |
 | Crossref | `Crossref_search_works` | 出版情報検索 |
 
+### 参照スキル
+
+| スキル | 連携 |
+|---|---|
+| `scientific-survival-clinical` | ← 生存解析・値引 HR |
+| `scientific-statistical-testing` | ← 仮説検定・効果量算出 |
+| `scientific-deep-research` | ← 系統的文献検索 |
+| `scientific-clinical-trials-analytics` | ← 臨床試験結果の統合 |
+| `scientific-academic-writing` | → メタアナリシス論文化 |
+
 #### 依存パッケージ
 
 ```