@nahisaho/satori 0.14.0 → 0.16.0

package/src/.github/skills/scientific-marine-ecology/SKILL.md

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+---
+name: scientific-marine-ecology
+description: |
+  海洋生態学統合スキル。OBIS 海洋生物分布・WoRMS 海洋分類体系・
+  GBIF 生物多様性レコード・FishBase 魚類データ。ToolUniverse
+  連携: obis, worms, gbif。
+tu_tools:
+  - key: obis
+    name: OBIS (Ocean Biodiversity Information System)
+    description: 海洋生物の出現・分布データを提供する国際プラットフォーム
+  - key: worms
+    name: WoRMS (World Register of Marine Species)
+    description: 海洋生物種の権威ある分類学的参照データベース
+  - key: gbif
+    name: GBIF (Global Biodiversity Information Facility)
+    description: 生物多様性データの国際的なオープンアクセスインフラ
+---
+
+# Scientific Marine Ecology
+
+OBIS / WoRMS / GBIF / FishBase を活用した海洋生物多様性・
+分布解析パイプラインを提供する。
+
+## When to Use
+
+- 海洋生物の地理的分布データを取得するとき
+- 海洋生物の分類学的情報 (WoRMS) を検証するとき
+- 生物多様性ホットスポットを解析するとき
+- 魚類の生態・形態データ (FishBase) を取得するとき
+- 海洋保全区域の生物多様性評価を行うとき
+- 海洋環境変動と種分布の関係を分析するとき
+
+---
+
+## Quick Start
+
+## 1. OBIS 海洋生物分布
+
+```python
+import requests
+import pandas as pd
+import numpy as np
+
+OBIS_BASE = "https://api.obis.org/v3"
+
+
+def obis_occurrence_search(taxon_name=None, taxon_id=None,
+                            geometry=None, year_range=None, limit=1000):
+    """
+    OBIS — 海洋生物出現記録検索。
+
+    Parameters:
+        taxon_name: str — 学名 (例: "Delphinidae")
+        taxon_id: int — AphiaID
+        geometry: str — WKT ジオメトリ (例: "POLYGON((...))")
+        year_range: tuple — (start_year, end_year)
+        limit: int — 最大取得件数
+    """
+    url = f"{OBIS_BASE}/occurrence"
+    params = {"size": min(limit, 5000)}
+
+    if taxon_name:
+        params["scientificname"] = taxon_name
+    if taxon_id:
+        params["taxonid"] = taxon_id
+    if geometry:
+        params["geometry"] = geometry
+    if year_range:
+        params["startdate"] = f"{year_range[0]}-01-01"
+        params["enddate"] = f"{year_range[1]}-12-31"
+
+    resp = requests.get(url, params=params, timeout=60)
+    resp.raise_for_status()
+    data = resp.json()
+
+    records = []
+    for rec in data.get("results", []):
+        records.append({
+            "scientific_name": rec.get("scientificName", ""),
+            "aphia_id": rec.get("aphiaID", ""),
+            "latitude": rec.get("decimalLatitude", None),
+            "longitude": rec.get("decimalLongitude", None),
+            "depth": rec.get("depth", None),
+            "date": rec.get("date_mid", ""),
+            "dataset_id": rec.get("dataset_id", ""),
+            "basis_of_record": rec.get("basisOfRecord", ""),
+        })
+
+    df = pd.DataFrame(records)
+    print(f"OBIS: '{taxon_name or taxon_id}' → {len(df)} occurrences")
+    return df
+
+
+def obis_checklist(geometry=None, area_id=None):
+    """
+    OBIS — 地域別種チェックリスト。
+
+    Parameters:
+        geometry: str — WKT ジオメトリ
+        area_id: int — OBIS エリア ID
+    """
+    url = f"{OBIS_BASE}/checklist"
+    params = {"size": 5000}
+    if geometry:
+        params["geometry"] = geometry
+    if area_id:
+        params["areaid"] = area_id
+
+    resp = requests.get(url, params=params, timeout=60)
+    resp.raise_for_status()
+    data = resp.json()
+
+    species = []
+    for sp in data.get("results", []):
+        species.append({
+            "scientific_name": sp.get("scientificName", ""),
+            "aphia_id": sp.get("taxonID", ""),
+            "records": sp.get("records", 0),
+            "kingdom": sp.get("kingdom", ""),
+            "phylum": sp.get("phylum", ""),
+            "class": sp.get("class", ""),
+            "order": sp.get("order", ""),
+            "family": sp.get("family", ""),
+        })
+
+    df = pd.DataFrame(species)
+    print(f"OBIS checklist: {len(df)} species")
+    return df
+```
+
+## 2. WoRMS 分類学検索
+
+```python
+WORMS_BASE = "https://www.marinespecies.org/rest"
+
+
+def worms_taxon_search(name, fuzzy=True, marine_only=True):
+    """
+    WoRMS — 海洋生物分類学的検索。
+
+    Parameters:
+        name: str — 種名/属名
+        fuzzy: bool — ファジー検索
+        marine_only: bool — 海洋種のみ
+    """
+    url = f"{WORMS_BASE}/AphiaRecordsByName/{name}"
+    params = {
+        "like": str(fuzzy).lower(),
+        "marine_only": str(marine_only).lower(),
+    }
+    resp = requests.get(url, params=params, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    results = []
+    for taxon in data if isinstance(data, list) else [data]:
+        results.append({
+            "aphia_id": taxon.get("AphiaID", ""),
+            "scientific_name": taxon.get("scientificname", ""),
+            "authority": taxon.get("authority", ""),
+            "status": taxon.get("status", ""),
+            "rank": taxon.get("rank", ""),
+            "valid_name": taxon.get("valid_name", ""),
+            "kingdom": taxon.get("kingdom", ""),
+            "phylum": taxon.get("phylum", ""),
+            "class": taxon.get("class", ""),
+            "order": taxon.get("order", ""),
+            "family": taxon.get("family", ""),
+            "genus": taxon.get("genus", ""),
+            "is_marine": taxon.get("isMarine", 0),
+            "is_brackish": taxon.get("isBrackish", 0),
+            "is_freshwater": taxon.get("isFreshwater", 0),
+        })
+
+    df = pd.DataFrame(results)
+    print(f"WoRMS: '{name}' → {len(df)} taxa")
+    return df
+
+
+def worms_classification(aphia_id):
+    """
+    WoRMS — 完全分類階層取得。
+
+    Parameters:
+        aphia_id: int — AphiaID
+    """
+    url = f"{WORMS_BASE}/AphiaClassificationByAphiaID/{aphia_id}"
+    resp = requests.get(url, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    hierarchy = []
+    node = data
+    while node:
+        hierarchy.append({
+            "aphia_id": node.get("AphiaID", ""),
+            "name": node.get("scientificname", ""),
+            "rank": node.get("rank", ""),
+        })
+        node = node.get("child")
+
+    df = pd.DataFrame(hierarchy)
+    print(f"WoRMS classification: {len(df)} levels")
+    return df
+```
+
+## 3. GBIF 生物多様性レコード
+
+```python
+GBIF_BASE = "https://api.gbif.org/v1"
+
+
+def gbif_species_search(name, limit=20):
+    """
+    GBIF — 種名検索・分類マッチング。
+
+    Parameters:
+        name: str — 種名
+        limit: int — 結果上限
+    """
+    url = f"{GBIF_BASE}/species/search"
+    params = {"q": name, "limit": limit}
+    resp = requests.get(url, params=params, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    results = []
+    for sp in data.get("results", []):
+        results.append({
+            "taxon_key": sp.get("key", ""),
+            "scientific_name": sp.get("scientificName", ""),
+            "canonical_name": sp.get("canonicalName", ""),
+            "status": sp.get("taxonomicStatus", ""),
+            "rank": sp.get("rank", ""),
+            "kingdom": sp.get("kingdom", ""),
+            "phylum": sp.get("phylum", ""),
+            "class": sp.get("class", ""),
+            "order": sp.get("order", ""),
+            "family": sp.get("family", ""),
+            "num_occurrences": sp.get("numOccurrences", 0),
+        })
+
+    df = pd.DataFrame(results)
+    print(f"GBIF species: '{name}' → {len(df)} taxa")
+    return df
+
+
+def gbif_occurrence_search(taxon_key=None, country=None,
+                            year_range=None, limit=300):
+    """
+    GBIF — 出現記録検索。
+
+    Parameters:
+        taxon_key: int — GBIF taxon key
+        country: str — ISO 国コード (例: "JP")
+        year_range: tuple — (start, end)
+        limit: int — 最大件数
+    """
+    url = f"{GBIF_BASE}/occurrence/search"
+    params = {"limit": min(limit, 300)}
+
+    if taxon_key:
+        params["taxonKey"] = taxon_key
+    if country:
+        params["country"] = country
+    if year_range:
+        params["year"] = f"{year_range[0]},{year_range[1]}"
+
+    resp = requests.get(url, params=params, timeout=60)
+    resp.raise_for_status()
+    data = resp.json()
+
+    records = []
+    for rec in data.get("results", []):
+        records.append({
+            "gbif_id": rec.get("gbifID", ""),
+            "scientific_name": rec.get("scientificName", ""),
+            "latitude": rec.get("decimalLatitude", None),
+            "longitude": rec.get("decimalLongitude", None),
+            "country": rec.get("country", ""),
+            "year": rec.get("year", ""),
+            "basis_of_record": rec.get("basisOfRecord", ""),
+            "institution": rec.get("institutionCode", ""),
+        })
+
+    df = pd.DataFrame(records)
+    print(f"GBIF occurrences: {len(df)} records (total: {data.get('count', 0)})")
+    return df
+```
+
+## 4. FishBase 魚類データ
+
+```python
+FISHBASE_BASE = "https://fishbase.ropensci.org"
+
+
+def fishbase_species(genus=None, species=None, family=None):
+    """
+    FishBase — 魚類種データ取得。
+
+    Parameters:
+        genus: str — 属名
+        species: str — 種小名
+        family: str — 科名
+    """
+    url = f"{FISHBASE_BASE}/species"
+    params = {"limit": 100}
+    if genus:
+        params["Genus"] = genus
+    if species:
+        params["Species"] = species
+    if family:
+        params["Family"] = family
+
+    resp = requests.get(url, params=params, timeout=30)
+    resp.raise_for_status()
+    data = resp.json()
+
+    records = []
+    for fish in data.get("data", []):
+        records.append({
+            "spec_code": fish.get("SpecCode", ""),
+            "genus": fish.get("Genus", ""),
+            "species": fish.get("Species", ""),
+            "family": fish.get("Family", ""),
+            "body_shape": fish.get("BodyShapeI", ""),
+            "max_length": fish.get("Length", None),
+            "vulnerability": fish.get("Vulnerability", None),
+            "importance": fish.get("Importance", ""),
+            "habitat": fish.get("DemersPelag", ""),
+            "depth_range": f"{fish.get('DepthRangeShallow', '')}-{fish.get('DepthRangeDeep', '')}",
+        })
+
+    df = pd.DataFrame(records)
+    print(f"FishBase: {len(df)} species")
+    return df
+```
+
+## 5. 海洋生態学統合パイプライン
+
+```python
+def marine_ecology_pipeline(taxon_name, region_wkt=None,
+                             output_dir="results"):
+    """
+    OBIS + WoRMS + GBIF + FishBase 統合パイプライン。
+
+    Parameters:
+        taxon_name: str — 分類群名
+        region_wkt: str — 調査海域 WKT
+        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) WoRMS 分類検証
+    taxonomy = worms_taxon_search(taxon_name)
+    taxonomy.to_csv(output_dir / "worms_taxonomy.csv", index=False)
+
+    aphia_id = None
+    if len(taxonomy) > 0:
+        aphia_id = taxonomy.iloc[0]["aphia_id"]
+        classification = worms_classification(aphia_id)
+        classification.to_csv(output_dir / "classification.csv", index=False)
+
+    # 2) OBIS 海洋分布
+    obis_data = obis_occurrence_search(
+        taxon_name=taxon_name,
+        taxon_id=aphia_id,
+        geometry=region_wkt,
+    )
+    obis_data.to_csv(output_dir / "obis_occurrences.csv", index=False)
+
+    # 3) GBIF 補完
+    gbif_sp = gbif_species_search(taxon_name)
+    if len(gbif_sp) > 0:
+        taxon_key = gbif_sp.iloc[0]["taxon_key"]
+        gbif_occ = gbif_occurrence_search(taxon_key=taxon_key)
+        gbif_occ.to_csv(output_dir / "gbif_occurrences.csv", index=False)
+    else:
+        gbif_occ = pd.DataFrame()
+
+    # 4) 多様性指標
+    if len(obis_data) > 0:
+        n_species = obis_data["scientific_name"].nunique()
+        lat_range = (obis_data["latitude"].min(), obis_data["latitude"].max())
+        depth_range = (obis_data["depth"].min(), obis_data["depth"].max())
+        print(f"Diversity: {n_species} species, "
+              f"lat {lat_range}, depth {depth_range}")
+
+    print(f"Marine ecology pipeline: {output_dir}")
+    return {
+        "taxonomy": taxonomy,
+        "obis_occurrences": obis_data,
+        "gbif_occurrences": gbif_occ,
+    }
+```
+
+---
+
+## ToolUniverse 連携
+
+| TU Key | ツール名 | 連携内容 |
+|--------|---------|---------|
+| `obis` | OBIS | 海洋生物出現・分布レコード検索 |
+| `worms` | WoRMS | 海洋種分類学的検証・階層取得 |
+| `gbif` | GBIF | 生物多様性出現レコード検索 |
+
+## パイプライン統合
+
+```
+environmental-ecology → marine-ecology → phylogenetics
+  (陸域生態学)          (OBIS/WoRMS/GBIF)  (系統解析)
+       │                      │               ↓
+  biodiversity-db ───────────┘         species-distribution
+  (ENA/BOLD)           │               (空間分布モデル)
+                       ↓
+                  fisheries-management
+                  (水産資源管理)
+```
+
+## パイプライン出力
+
+| ファイル | 説明 | 次スキル |
+|---------|------|---------|
+| `results/worms_taxonomy.csv` | WoRMS 分類情報 | → phylogenetics |
+| `results/obis_occurrences.csv` | OBIS 出現記録 | → species-distribution |
+| `results/gbif_occurrences.csv` | GBIF 出現記録 | → biodiversity-db |
+| `results/classification.csv` | 分類階層 | → environmental-ecology |