@nahisaho/satori 0.13.0 → 0.14.0

package/src/.github/skills/scientific-preprint-archive/SKILL.md

@@ -0,0 +1,476 @@
+---
+name: scientific-preprint-archive
+description: |
+  プレプリント・オープンアクセスアーカイブ検索スキル。bioRxiv/medRxiv
+  プレプリント検索、arXiv 論文取得、PMC フルテキスト、DOAJ OA ジャーナル、
+  Unpaywall OA リンク、CORE/HAL/Zenodo/OpenAIRE/OSF/Fatcat/DBLP
+  統合文献アクセスパイプライン。
+---
+
+# Scientific Preprint Archive
+
+bioRxiv / medRxiv / arXiv / PMC / DOAJ / Unpaywall / CORE / HAL /
+Zenodo / OpenAIRE / OSF Preprints / Fatcat / DBLP を統合した
+プレプリント・オープンアクセス文献検索パイプラインを提供する。
+
+## When to Use
+
+- 最新のプレプリントを bioRxiv / medRxiv から検索するとき
+- arXiv の機械学習・計算科学論文を取得するとき
+- PMC フルテキスト XML を取得してテキストマイニングするとき
+- OA 版のリンクを Unpaywall で見つけるとき
+- CORE / Zenodo / OpenAIRE など複数アーカイブを横断検索するとき
+- 系統的レビューの文献収集で網羅的プレプリント検索が必要なとき
+- DBLP から計算機科学文献メタデータを取得するとき
+
+---
+
+## Quick Start
+
+## 1. bioRxiv / medRxiv プレプリント検索
+
+```python
+import requests
+import pandas as pd
+from datetime import datetime, timedelta
+
+BIORXIV_API = "https://api.biorxiv.org"
+
+
+def search_biorxiv(query, server="biorxiv", days=30, cursor=0):
+    """
+    bioRxiv/medRxiv プレプリント検索。
+
+    Parameters:
+        query: str — 検索クエリ
+        server: str — "biorxiv" or "medrxiv"
+        days: int — 過去何日分を検索するか
+        cursor: int — ページネーション offset
+
+    ToolUniverse:
+        bioRxiv_search_preprints(query=query, server=server)
+        bioRxiv_get_preprint_details(doi=doi)
+        medRxiv_search_preprints(query=query)
+    """
+    end_date = datetime.now().strftime("%Y-%m-%d")
+    start_date = (datetime.now() - timedelta(days=days)).strftime("%Y-%m-%d")
+
+    url = f"{BIORXIV_API}/details/{server}/{start_date}/{end_date}/{cursor}"
+    resp = requests.get(url)
+    resp.raise_for_status()
+    data = resp.json()
+
+    results = []
+    for paper in data.get("collection", []):
+        title = paper.get("title", "").lower()
+        abstract = paper.get("abstract", "").lower()
+        if query.lower() in title or query.lower() in abstract:
+            results.append({
+                "doi": paper.get("doi", ""),
+                "title": paper.get("title", ""),
+                "authors": paper.get("authors", ""),
+                "date": paper.get("date", ""),
+                "category": paper.get("category", ""),
+                "server": server,
+                "abstract": paper.get("abstract", "")[:300],
+            })
+
+    df = pd.DataFrame(results)
+    print(f"{server} search '{query}': {len(df)} preprints (last {days} days)")
+    return df
+```
+
+## 2. arXiv 論文検索
+
+```python
+import urllib.parse
+import xml.etree.ElementTree as ET
+
+ARXIV_API = "http://export.arxiv.org/api/query"
+
+
+def search_arxiv(query, category=None, max_results=50, sort_by="submittedDate"):
+    """
+    arXiv 論文検索。
+
+    Parameters:
+        query: str — 検索クエリ
+        category: str — arXiv カテゴリ (e.g., "q-bio.GN", "cs.LG", "stat.ML")
+        max_results: int — 最大取得数
+        sort_by: str — "submittedDate", "lastUpdatedDate", "relevance"
+
+    ToolUniverse:
+        arXiv_search_papers(query=query, category=category)
+        arXiv_get_paper(arxiv_id=arxiv_id)
+    """
+    search_query = f"all:{query}"
+    if category:
+        search_query += f"+AND+cat:{category}"
+
+    params = {
+        "search_query": search_query,
+        "start": 0,
+        "max_results": max_results,
+        "sortBy": sort_by,
+        "sortOrder": "descending",
+    }
+    resp = requests.get(ARXIV_API, params=params)
+    resp.raise_for_status()
+
+    ns = {"atom": "http://www.w3.org/2005/Atom", "arxiv": "http://arxiv.org/schemas/atom"}
+    root = ET.fromstring(resp.text)
+
+    results = []
+    for entry in root.findall("atom:entry", ns):
+        categories = [c.get("term") for c in entry.findall("atom:category", ns)]
+        results.append({
+            "arxiv_id": entry.find("atom:id", ns).text.split("/abs/")[-1],
+            "title": entry.find("atom:title", ns).text.strip().replace("\n", " "),
+            "authors": ", ".join(
+                a.find("atom:name", ns).text
+                for a in entry.findall("atom:author", ns)
+            ),
+            "published": entry.find("atom:published", ns).text[:10],
+            "categories": categories,
+            "abstract": entry.find("atom:summary", ns).text.strip()[:300],
+            "pdf_url": next(
+                (l.get("href") for l in entry.findall("atom:link", ns)
+                 if l.get("title") == "pdf"), ""
+            ),
+        })
+
+    df = pd.DataFrame(results)
+    cat_str = f" [{category}]" if category else ""
+    print(f"arXiv search '{query}'{cat_str}: {len(df)} papers")
+    return df
+```
+
+## 3. PMC フルテキストアクセス
+
+```python
+PMC_API = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils"
+
+
+def get_pmc_fulltext(pmcid, email="user@example.com"):
+    """
+    PMC フルテキスト XML 取得。
+
+    Parameters:
+        pmcid: str — PMC ID (e.g., "PMC1234567")
+        email: str — NCBI API 用メールアドレス
+
+    ToolUniverse:
+        PMC_get_fulltext(pmcid=pmcid)
+    """
+    params = {
+        "db": "pmc",
+        "id": pmcid.replace("PMC", ""),
+        "rettype": "xml",
+        "email": email,
+    }
+    resp = requests.get(f"{PMC_API}/efetch.fcgi", params=params)
+    resp.raise_for_status()
+
+    root = ET.fromstring(resp.text)
+    article = root.find(".//article")
+
+    sections = {}
+    for sec in article.findall(".//sec") if article is not None else []:
+        title = sec.find("title")
+        if title is not None and title.text:
+            paragraphs = [p.text for p in sec.findall("p") if p.text]
+            sections[title.text] = " ".join(paragraphs)
+
+    print(f"PMC {pmcid}: {len(sections)} sections retrieved")
+    return sections
+```
+
+## 4. Unpaywall OA リンク検索
+
+```python
+UNPAYWALL_API = "https://api.unpaywall.org/v2"
+
+
+def find_oa_version(doi, email="user@example.com"):
+    """
+    Unpaywall で論文の OA 版リンクを検索。
+
+    Parameters:
+        doi: str — DOI
+        email: str — API 利用者メール
+
+    ToolUniverse:
+        Unpaywall_get_oa_status(doi=doi)
+    """
+    resp = requests.get(f"{UNPAYWALL_API}/{doi}", params={"email": email})
+    resp.raise_for_status()
+    data = resp.json()
+
+    oa_locations = data.get("oa_locations", [])
+    result = {
+        "doi": doi,
+        "is_oa": data.get("is_oa", False),
+        "oa_status": data.get("oa_status", ""),
+        "best_oa_url": data.get("best_oa_location", {}).get("url_for_pdf", ""),
+        "journal": data.get("journal_name", ""),
+        "publisher": data.get("publisher", ""),
+        "n_oa_locations": len(oa_locations),
+        "locations": [
+            {
+                "url": loc.get("url_for_pdf") or loc.get("url"),
+                "host_type": loc.get("host_type"),
+                "version": loc.get("version"),
+            }
+            for loc in oa_locations
+        ],
+    }
+    print(f"Unpaywall {doi}: OA={result['is_oa']}, status={result['oa_status']}")
+    return result
+```
+
+## 5. CORE 統合検索
+
+```python
+CORE_API = "https://api.core.ac.uk/v3"
+
+
+def search_core(query, api_key, limit=25):
+    """
+    CORE リポジトリ横断検索 (1.4 億+ 論文)。
+
+    Parameters:
+        query: str — 検索クエリ
+        api_key: str — CORE API キー
+        limit: int — 最大取得数
+
+    ToolUniverse:
+        CORE_search_works(query=query)
+        CORE_get_work(core_id=core_id)
+    """
+    headers = {"Authorization": f"Bearer {api_key}"}
+    params = {"q": query, "limit": limit}
+    resp = requests.get(f"{CORE_API}/search/works", headers=headers, params=params)
+    resp.raise_for_status()
+    data = resp.json()
+
+    results = []
+    for work in data.get("results", []):
+        results.append({
+            "core_id": work.get("id", ""),
+            "title": work.get("title", ""),
+            "authors": ", ".join(
+                a.get("name", "") for a in work.get("authors", [])
+            ),
+            "year": work.get("yearPublished", ""),
+            "doi": work.get("doi", ""),
+            "download_url": work.get("downloadUrl", ""),
+            "abstract": (work.get("abstract") or "")[:300],
+        })
+
+    df = pd.DataFrame(results)
+    print(f"CORE search '{query}': {len(df)} works")
+    return df
+```
+
+## 6. Zenodo レコード検索
+
+```python
+ZENODO_API = "https://zenodo.org/api"
+
+
+def search_zenodo(query, resource_type=None, size=25):
+    """
+    Zenodo レコード検索 (データセット・ソフトウェア・論文)。
+
+    Parameters:
+        query: str — 検索クエリ
+        resource_type: str — "publication", "dataset", "software", "poster"
+        size: int — 最大取得数
+
+    ToolUniverse:
+        Zenodo_search_records(query=query, type=resource_type)
+    """
+    params = {"q": query, "size": size}
+    if resource_type:
+        params["type"] = resource_type
+    resp = requests.get(f"{ZENODO_API}/records", params=params)
+    resp.raise_for_status()
+    data = resp.json()
+
+    results = []
+    for hit in data.get("hits", {}).get("hits", []):
+        meta = hit.get("metadata", {})
+        results.append({
+            "zenodo_id": hit.get("id", ""),
+            "doi": meta.get("doi", ""),
+            "title": meta.get("title", ""),
+            "creators": ", ".join(
+                c.get("name", "") for c in meta.get("creators", [])
+            ),
+            "resource_type": meta.get("resource_type", {}).get("type", ""),
+            "publication_date": meta.get("publication_date", ""),
+            "access_right": meta.get("access_right", ""),
+        })
+
+    df = pd.DataFrame(results)
+    print(f"Zenodo search '{query}': {len(df)} records")
+    return df
+```
+
+## 7. DOAJ OA ジャーナル検索
+
+```python
+DOAJ_API = "https://doaj.org/api"
+
+
+def search_doaj_articles(query, page=1, page_size=25):
+    """
+    DOAJ OA ジャーナル記事検索。
+
+    ToolUniverse:
+        DOAJ_search_articles(query=query)
+    """
+    params = {"q": query, "page": page, "pageSize": page_size}
+    resp = requests.get(f"{DOAJ_API}/search/articles/{query}")
+    resp.raise_for_status()
+    data = resp.json()
+
+    results = []
+    for item in data.get("results", []):
+        bib = item.get("bibjson", {})
+        results.append({
+            "doi": bib.get("identifier", [{}])[0].get("id", ""),
+            "title": bib.get("title", ""),
+            "journal": bib.get("journal", {}).get("title", ""),
+            "year": bib.get("year", ""),
+            "authors": ", ".join(
+                a.get("name", "") for a in bib.get("author", [])
+            ),
+            "keywords": bib.get("keywords", []),
+        })
+
+    df = pd.DataFrame(results)
+    print(f"DOAJ search '{query}': {len(df)} OA articles")
+    return df
+```
+
+## 8. OpenAIRE 研究成果物検索
+
+```python
+OPENAIRE_API = "https://api.openaire.eu/search"
+
+
+def search_openaire(query, result_type="publication", size=25):
+    """
+    OpenAIRE 研究成果物検索 (EU 助成研究中心)。
+
+    ToolUniverse:
+        OpenAIRE_search_publications(query=query)
+    """
+    params = {
+        "keywords": query,
+        "size": size,
+        "format": "json",
+    }
+    resp = requests.get(f"{OPENAIRE_API}/{result_type}s", params=params)
+    resp.raise_for_status()
+    data = resp.json()
+
+    results_list = (
+        data.get("response", {}).get("results", {}).get("result", [])
+    )
+    results = []
+    for item in results_list:
+        meta = item.get("metadata", {}).get("oaf:entity", {}).get("oaf:result", {})
+        results.append({
+            "title": meta.get("title", {}).get("$", ""),
+            "date": meta.get("dateofacceptance", {}).get("$", ""),
+            "publisher": meta.get("publisher", {}).get("$", ""),
+        })
+
+    df = pd.DataFrame(results)
+    print(f"OpenAIRE search '{query}': {len(df)} results")
+    return df
+```
+
+## 9. 統合マルチアーカイブ検索パイプライン
+
+```python
+def multi_archive_search(query, archives=None, **kwargs):
+    """
+    複数プレプリント/OA アーカイブ横断検索。
+
+    Parameters:
+        query: str — 検索クエリ
+        archives: list — ["biorxiv", "medrxiv", "arxiv", "core", "zenodo", "doaj", "openaire"]
+    """
+    if archives is None:
+        archives = ["biorxiv", "arxiv", "core"]
+
+    all_results = {}
+    search_funcs = {
+        "biorxiv": lambda q: search_biorxiv(q, server="biorxiv"),
+        "medrxiv": lambda q: search_biorxiv(q, server="medrxiv"),
+        "arxiv": lambda q: search_arxiv(q),
+        "core": lambda q: search_core(q, api_key=kwargs.get("core_api_key", "")),
+        "zenodo": lambda q: search_zenodo(q),
+        "doaj": lambda q: search_doaj_articles(q),
+        "openaire": lambda q: search_openaire(q),
+    }
+
+    for archive in archives:
+        if archive in search_funcs:
+            try:
+                df = search_funcs[archive](query)
+                all_results[archive] = df
+                print(f"  ✓ {archive}: {len(df)} results")
+            except Exception as e:
+                print(f"  ✗ {archive}: {e}")
+                all_results[archive] = pd.DataFrame()
+
+    total = sum(len(df) for df in all_results.values())
+    print(f"\nTotal: {total} results across {len(archives)} archives")
+    return all_results
+```
+
+---
+
+## 利用可能ツール
+
+以下のツールが ToolUniverse SMCP 経由で利用可能:
+
+| ToolUniverse カテゴリ | 主なツール |
+|---|---|
+| `biorxiv` | `bioRxiv_search_preprints`, `bioRxiv_get_preprint_details` |
+| `medrxiv` | `medRxiv_search_preprints` |
+| `arxiv` | `arXiv_search_papers`, `arXiv_get_paper` |
+| `pmc` | `PMC_get_fulltext` |
+| `doaj` | `DOAJ_search_articles` |
+| `unpaywall` | `Unpaywall_get_oa_status` |
+| `hal` | `HAL_search` |
+| `core` | `CORE_search_works`, `CORE_get_work` |
+| `zenodo` | `Zenodo_search_records` |
+| `openaire` | `OpenAIRE_search_publications` |
+| `osf_preprints` | `OSF_search_preprints` |
+| `fatcat` | `Fatcat_search_releases` |
+| `dblp` | `DBLP_search_publications` |
+
+## パイプライン出力
+
+| 出力ファイル | 説明 | 連携先スキル |
+|---|---|---|
+| `results/preprint_search.csv` | 横断検索結果 | → literature-search, systematic-review |
+| `results/oa_availability.json` | OA ステータス・リンク | → deep-research |
+| `results/fulltext_corpus/` | フルテキストコーパス | → text-mining-nlp, biomedical-pubtator |
+| `results/arxiv_papers.csv` | arXiv 論文メタデータ | → deep-learning, graph-neural-networks |
+
+## パイプライン統合
+
+```
+literature-search ──→ preprint-archive ──→ systematic-review
+  (PubMed/OpenAlex)   (bioRxiv/arXiv/CORE)  (PRISMA 2020)
+                              │
+                              ├──→ text-mining-nlp (NER/KG)
+                              ├──→ biomedical-pubtator (PubTator NER)
+                              └──→ deep-research (エビデンス統合)
+```