@nahisaho/satori 0.12.0 → 0.13.0

package/src/.github/skills/scientific-structural-proteomics/SKILL.md

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+---
+name: scientific-structural-proteomics
+description: |
+  構造プロテオミクス統合スキル。EMDB クライオ EM、PDBe 構造データ、
+  Proteins API (UniProt)、Complex Portal 複合体、DeepGO 機能予測、
+  EVE 変異影響評価の統合パイプライン。
+---
+
+# Scientific Structural Proteomics
+
+6 つの構造・機能データベースを統合した
+タンパク質構造・機能プロファイリングパイプラインを提供する。
+
+## When to Use
+
+- PDB エントリの詳細構造情報 (分解能, 実験手法, 二次構造) を取得するとき
+- クライオ EM マップ情報を EMDB から取得するとき
+- UniProt タンパク質のドメイン・変異・ゲノムマッピングを調べるとき
+- タンパク質複合体のサブユニット構成を Complex Portal で調べるとき
+- DeepGO で配列ベースの GO 機能予測を行うとき
+- EVE で missense 変異の病原性スコアを取得するとき
+
+---
+
+## Quick Start
+
+## 1. PDBe 構造データ取得
+
+```python
+import requests
+import pandas as pd
+
+PDBE_API = "https://www.ebi.ac.uk/pdbe/api"
+
+
+def get_pdbe_entry(pdb_id):
+    """
+    PDBe エントリのサマリー・品質・二次構造を取得。
+
+    Parameters:
+        pdb_id: str — PDB ID (e.g., "1cbs")
+
+    ToolUniverse:
+        pdbe_get_entry_summary(pdb_id=pdb_id)
+        pdbe_get_entry_quality(pdb_id=pdb_id)
+        pdbe_get_entry_experiment(pdb_id=pdb_id)
+        pdbe_get_entry_molecules(pdb_id=pdb_id)
+        pdbe_get_entry_secondary_structure(pdb_id=pdb_id)
+        pdbe_get_entry_assemblies(pdb_id=pdb_id)
+        pdbe_get_entry_publications(pdb_id=pdb_id)
+    """
+    pdb = pdb_id.lower()
+
+    # Summary
+    resp_s = requests.get(f"{PDBE_API}/pdb/entry/summary/{pdb}")
+    resp_s.raise_for_status()
+    summary = resp_s.json().get(pdb, [{}])[0]
+
+    # Quality
+    resp_q = requests.get(f"{PDBE_API}/pdb/entry/quality/{pdb}")
+    quality = (
+        resp_q.json().get(pdb, [{}])[0] if resp_q.status_code == 200 else {}
+    )
+
+    # Experiment
+    resp_e = requests.get(f"{PDBE_API}/pdb/entry/experiment/{pdb}")
+    experiment = (
+        resp_e.json().get(pdb, [{}])[0] if resp_e.status_code == 200 else {}
+    )
+
+    entry = {
+        "pdb_id": pdb,
+        "title": summary.get("title", ""),
+        "method": experiment.get("experimental_method", ""),
+        "resolution": experiment.get("resolution", ""),
+        "release_date": summary.get("release_date", ""),
+        "r_factor": quality.get("r_factor", ""),
+        "r_free": quality.get("r_free", ""),
+    }
+
+    print(f"PDBe {pdb}: {entry['method']} @ {entry['resolution']}Å")
+    return entry, summary, quality
+```
+
+## 2. EMDB クライオ EM 構造
+
+```python
+EMDB_API = "https://www.ebi.ac.uk/emdb/api"
+
+
+def get_emdb_structure(emdb_id):
+    """
+    EMDB エントリの 3D EM マップ情報を取得。
+
+    Parameters:
+        emdb_id: str — EMDB ID (e.g., "EMD-1234")
+
+    ToolUniverse:
+        EMDB_get_structure(emdb_id=emdb_id)
+        EMDB_get_map_info(emdb_id=emdb_id)
+        EMDB_get_sample_info(emdb_id=emdb_id)
+        EMDB_get_imaging_info(emdb_id=emdb_id)
+        EMDB_get_validation(emdb_id=emdb_id)
+        EMDB_get_publications(emdb_id=emdb_id)
+        EMDB_search_structures(query=query)
+    """
+    url = f"{EMDB_API}/entry/{emdb_id}"
+    resp = requests.get(url)
+    resp.raise_for_status()
+    data = resp.json()
+
+    admin = data.get("admin", {})
+    map_info = data.get("map", {})
+
+    entry = {
+        "emdb_id": emdb_id,
+        "title": admin.get("title", ""),
+        "resolution": map_info.get("resolution", {}).get("value", ""),
+        "contour_level": map_info.get("contour_level", {}).get("value", ""),
+        "deposition_date": admin.get("deposition_date", ""),
+    }
+
+    print(f"EMDB {emdb_id}: {entry['resolution']}Å resolution")
+    return entry, data
+```
+
+## 3. Proteins API (UniProt) ドメイン・変異
+
+```python
+PROTEINS_API = "https://www.ebi.ac.uk/proteins/api"
+
+
+def get_protein_features(uniprot_id):
+    """
+    Proteins API からタンパク質のドメイン・変異・修飾情報を取得。
+
+    Parameters:
+        uniprot_id: str — UniProt accession (e.g., "P04637")
+
+    ToolUniverse:
+        proteins_api_get_protein(accession=uniprot_id)
+        proteins_api_get_features(accession=uniprot_id)
+        proteins_api_get_variants(accession=uniprot_id)
+        proteins_api_get_xrefs(accession=uniprot_id)
+        proteins_api_get_genome_mappings(accession=uniprot_id)
+    """
+    headers = {"Accept": "application/json"}
+
+    # Protein info
+    resp_p = requests.get(
+        f"{PROTEINS_API}/proteins/{uniprot_id}", headers=headers
+    )
+    resp_p.raise_for_status()
+    protein = resp_p.json()
+
+    # Features
+    resp_f = requests.get(
+        f"{PROTEINS_API}/features/{uniprot_id}", headers=headers
+    )
+    features = resp_f.json() if resp_f.status_code == 200 else {}
+
+    feature_list = features.get("features", [])
+    domains = [f for f in feature_list if f.get("type") == "DOMAIN"]
+    variants = [f for f in feature_list if f.get("type") == "VARIANT"]
+
+    print(f"Proteins API {uniprot_id}: "
+          f"{len(domains)} domains, {len(variants)} variants")
+    return protein, feature_list
+```
+
+## 4. Complex Portal 複合体
+
+```python
+def get_complex_portal(complex_id):
+    """
+    Complex Portal からタンパク質複合体の詳細を取得。
+
+    Parameters:
+        complex_id: str — Complex Portal ID (e.g., "CPX-1")
+
+    ToolUniverse:
+        ComplexPortal_get_complex(complex_id=complex_id)
+        ComplexPortal_search_complexes(query=query)
+    """
+    url = (
+        f"https://www.ebi.ac.uk/intact/complex-ws/complex/{complex_id}"
+    )
+    resp = requests.get(url, headers={"Accept": "application/json"})
+    resp.raise_for_status()
+    data = resp.json()
+
+    participants = data.get("participants", [])
+    subunits = []
+    for p in participants:
+        interactor = p.get("interactor", {})
+        subunits.append({
+            "identifier": interactor.get("identifier", ""),
+            "name": interactor.get("name", ""),
+            "stoichiometry": p.get("stoichiometry", ""),
+        })
+
+    print(f"Complex Portal {complex_id}: "
+          f"{data.get('name', '?')}, {len(subunits)} subunits")
+    return data, subunits
+```
+
+## 5. DeepGO 機能予測 & EVE 変異評価
+
+```python
+def predict_deepgo_function(sequence):
+    """
+    DeepGO でタンパク質配列から GO 機能予測。
+
+    ToolUniverse:
+        DeepGO_predict_function(sequence=sequence)
+    """
+    url = "https://deepgo.cbrc.kaust.edu.sa/deepgo/api/create"
+    resp = requests.post(url, json={"data_format": "fasta", "data": sequence})
+    resp.raise_for_status()
+    data = resp.json()
+
+    predictions = data.get("predictions", [])
+    print(f"DeepGO: {len(predictions)} GO term predictions")
+    return predictions
+
+
+def get_eve_variant_score(gene_name, variant=None):
+    """
+    EVE (Evolutionary model of Variant Effect) による
+    missense 変異の病原性スコアを取得。
+
+    ToolUniverse:
+        EVE_get_gene_info(gene_name=gene_name)
+        EVE_get_variant_score(gene_name=gene_name, variant=variant)
+    """
+    url = f"https://evemodel.org/api/proteins/{gene_name}"
+
+    if variant:
+        url += f"/variants/{variant}"
+
+    resp = requests.get(url)
+    resp.raise_for_status()
+    data = resp.json()
+
+    if variant:
+        score = data.get("eve_score", None)
+        classification = data.get("eve_class", "")
+        print(f"EVE {gene_name} {variant}: score={score}, class={classification}")
+    else:
+        print(f"EVE {gene_name}: found")
+
+    return data
+```
+
+## References
+
+### Output Files
+
+| ファイル | 形式 |
+|---|---|
+| `results/pdbe_entry.json` | JSON |
+| `results/emdb_structure.json` | JSON |
+| `results/protein_features.json` | JSON |
+| `results/complex_portal.json` | JSON |
+| `results/deepgo_predictions.json` | JSON |
+| `results/eve_scores.json` | JSON |
+
+### 利用可能ツール
+
+| カテゴリ | 主要ツール | 用途 |
+|---|---|---|
+| PDBe | `pdbe_get_entry_summary` | エントリサマリー |
+| PDBe | `pdbe_get_entry_quality` | 構造品質 |
+| PDBe | `pdbe_get_entry_experiment` | 実験手法 |
+| PDBe | `pdbe_get_entry_molecules` | 分子情報 |
+| PDBe | `pdbe_get_entry_secondary_structure` | 二次構造 |
+| PDBe | `pdbe_get_entry_assemblies` | 生物学的集合体 |
+| PDBe | `pdbe_get_entry_publications` | 文献 |
+| PDBe | `pdbe_get_entry_related_publications` | 関連文献 |
+| PDBe | `pdbe_get_entry_observed_residues_ratio` | 観察残基 |
+| PDBe | `pdbe_get_entry_status` | ステータス |
+| EMDB | `EMDB_get_structure` | EM 構造 |
+| EMDB | `EMDB_get_map_info` | マップ情報 |
+| EMDB | `EMDB_get_sample_info` | サンプル情報 |
+| EMDB | `EMDB_get_imaging_info` | イメージング |
+| EMDB | `EMDB_get_validation` | バリデーション |
+| EMDB | `EMDB_get_publications` | 文献 |
+| EMDB | `EMDB_search_structures` | EM 構造検索 |
+| Proteins API | `proteins_api_get_protein` | タンパク質情報 |
+| Proteins API | `proteins_api_get_features` | ドメイン・特徴 |
+| Proteins API | `proteins_api_get_variants` | 変異 |
+| Proteins API | `proteins_api_get_xrefs` | 外部参照 |
+| Proteins API | `proteins_api_get_genome_mappings` | ゲノムマッピング |
+| Proteins API | `proteins_api_get_epitopes` | エピトープ |
+| Proteins API | `proteins_api_get_proteomics` | プロテオミクス |
+| Proteins API | `proteins_api_get_publications` | 文献 |
+| Proteins API | `proteins_api_get_comments` | コメント |
+| Proteins API | `proteins_api_search` | 検索 |
+| Complex Portal | `ComplexPortal_get_complex` | 複合体詳細 |
+| Complex Portal | `ComplexPortal_search_complexes` | 複合体検索 |
+| DeepGO | `DeepGO_predict_function` | GO 機能予測 |
+| EVE | `EVE_get_gene_info` | 遺伝子情報 |
+| EVE | `EVE_get_variant_score` | 変異スコア |
+
+### 参照スキル
+
+| スキル | 関連 |
+|---|---|
+| `scientific-protein-structure-analysis` | タンパク質構造 |
+| `scientific-proteomics-mass-spectrometry` | プロテオミクス |
+| `scientific-protein-interaction-network` | PPI |
+| `scientific-molecular-docking` | ドッキング |
+| `scientific-variant-interpretation` | 変異解釈 |
+
+### 依存パッケージ
+
+`requests`, `pandas`