@nahisaho/satori 0.12.0 → 0.14.0

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`

package/src/.github/skills/scientific-symbolic-mathematics/SKILL.md

@@ -0,0 +1,277 @@
+---
+name: scientific-symbolic-mathematics
+description: |
+  記号数学スキル。SymPy による解析的微積分・線形代数・微分方程式求解、
+  記号式の LaTeX 変換、数値計算との統合、科学モデリング用
+  記号計算パイプライン。
+---
+
+# Scientific Symbolic Mathematics
+
+SymPy を中心とした記号数学 (Computer Algebra System)
+パイプラインを提供する。
+
+## When to Use
+
+- 微分方程式を解析的に解くとき
+- 数式の記号的微分・積分を行うとき
+- 行列の固有値・固有ベクトルを記号的に求めるとき
+- 科学モデルのパラメータに関する感度解析を記号的に行うとき
+- 数式を LaTeX 形式に変換するとき
+- 記号解と数値解を比較検証するとき
+
+---
+
+## Quick Start
+
+## 1. 微分方程式の解析解
+
+```python
+import sympy as sp
+from sympy import (
+    symbols, Function, Eq, dsolve, classify_ode,
+    exp, sin, cos, sqrt, pi, oo, integrate, diff,
+    Matrix, latex, simplify, factor, expand, solve,
+    Rational, Sum, Product, series,
+)
+import numpy as np
+
+
+def solve_ode(ode_expr, dependent_var, independent_var, ics=None):
+    """
+    常微分方程式の解析解。
+
+    Parameters:
+        ode_expr: sympy.Eq — ODE (e.g., Eq(f(x).diff(x, 2) + f(x), 0))
+        dependent_var: sympy.Function — 従属変数
+        independent_var: sympy.Symbol — 独立変数
+        ics: dict — 初期条件 {f(0): 1, f'(0): 0}
+
+    K-Dense: sympy — Symbolic mathematics
+    """
+    # Classify ODE
+    classification = classify_ode(ode_expr, dependent_var(independent_var))
+    print(f"ODE classification: {classification[:3]}")
+
+    # Solve
+    solution = dsolve(ode_expr, dependent_var(independent_var), ics=ics)
+
+    print(f"Solution: {solution}")
+    print(f"LaTeX: {latex(solution)}")
+    return solution
+
+
+# Example: damped harmonic oscillator
+x, t, omega, gamma = symbols("x t omega gamma", positive=True)
+f = Function("f")
+
+# f''(t) + 2γf'(t) + ω²f(t) = 0
+damped_ode = Eq(f(t).diff(t, 2) + 2*gamma*f(t).diff(t) + omega**2*f(t), 0)
+```
+
+## 2. 記号的微積分
+
+```python
+def symbolic_calculus(expr, var, operations=None):
+    """
+    記号的微積分操作。
+
+    Parameters:
+        expr: sympy expression — 数式
+        var: sympy.Symbol — 変数
+        operations: list — ["diff", "integrate", "series", "limit"]
+    """
+    if operations is None:
+        operations = ["diff", "integrate"]
+
+    results = {}
+
+    if "diff" in operations:
+        deriv = diff(expr, var)
+        results["derivative"] = {"expr": deriv, "latex": latex(deriv)}
+        print(f"d/d{var}({expr}) = {deriv}")
+
+    if "integrate" in operations:
+        integral = integrate(expr, var)
+        results["integral"] = {"expr": integral, "latex": latex(integral)}
+        print(f"∫{expr} d{var} = {integral}")
+
+    if "series" in operations:
+        ser = series(expr, var, 0, n=6)
+        results["series"] = {"expr": ser, "latex": latex(ser)}
+        print(f"Taylor series: {ser}")
+
+    if "limit" in operations:
+        from sympy import limit as sp_limit
+        lim = sp_limit(expr, var, oo)
+        results["limit"] = {"expr": lim, "latex": latex(lim)}
+        print(f"lim({var}→∞) {expr} = {lim}")
+
+    return results
+```
+
+## 3. 線形代数 (記号的)
+
+```python
+def symbolic_linear_algebra(matrix_data):
+    """
+    記号的線形代数 — 固有値・固有ベクトル・行列分解。
+
+    Parameters:
+        matrix_data: list of lists — 行列要素 (記号含む)
+    """
+    M = Matrix(matrix_data)
+    print(f"Matrix ({M.rows}×{M.cols}):")
+    sp.pprint(M)
+
+    results = {}
+
+    # Determinant
+    det = M.det()
+    results["determinant"] = {"expr": det, "latex": latex(det)}
+    print(f"\nDeterminant: {det}")
+
+    # Eigenvalues & eigenvectors
+    eigenvals = M.eigenvals()
+    results["eigenvalues"] = {str(k): v for k, v in eigenvals.items()}
+    print(f"Eigenvalues: {eigenvals}")
+
+    eigenvects = M.eigenvects()
+    results["eigenvectors"] = [
+        {"eigenvalue": str(ev[0]), "multiplicity": ev[1],
+         "vectors": [str(v) for v in ev[2]]}
+        for ev in eigenvects
+    ]
+
+    # Characteristic polynomial
+    lam = symbols("lambda")
+    char_poly = M.charpoly(lam)
+    results["characteristic_polynomial"] = {
+        "expr": str(char_poly.as_expr()),
+        "latex": latex(char_poly.as_expr()),
+    }
+    print(f"Characteristic polynomial: {char_poly.as_expr()}")
+
+    # Inverse (if nonsingular)
+    if det != 0:
+        inv = M.inv()
+        results["inverse"] = {"latex": latex(inv)}
+        print(f"Inverse exists: {M.rows}×{M.cols}")
+
+    return results
+```
+
+## 4. 科学モデリング (薬物動態学 PK モデル例)
+
+```python
+def pk_compartment_model(n_compartments=1):
+    """
+    薬物動態学コンパートメントモデルの記号的解法。
+
+    Parameters:
+        n_compartments: int — 1 (1-compartment) or 2 (2-compartment)
+    """
+    t = symbols("t", positive=True)
+
+    if n_compartments == 1:
+        # 1-compartment: dC/dt = -ke * C
+        C = Function("C")
+        ke, C0 = symbols("k_e C_0", positive=True)
+        ode = Eq(C(t).diff(t), -ke * C(t))
+        solution = dsolve(ode, C(t), ics={C(0): C0})
+
+        # Half-life
+        t_half = sp.solve(Eq(solution.rhs, C0/2), t)[0]
+
+        # AUC (0→∞)
+        auc = integrate(solution.rhs, (t, 0, oo))
+
+        result = {
+            "model": "1-compartment IV bolus",
+            "ode": latex(ode),
+            "solution": latex(solution),
+            "half_life": latex(t_half),
+            "auc_inf": latex(auc),
+        }
+        print(f"PK 1-compartment: C(t) = {solution.rhs}")
+        print(f"  t½ = {t_half}")
+        print(f"  AUC(0→∞) = {auc}")
+
+    elif n_compartments == 2:
+        # 2-compartment model
+        C1, C2 = Function("C1"), Function("C2")
+        k10, k12, k21, D, V1 = symbols("k_10 k_12 k_21 D V_1", positive=True)
+
+        ode1 = Eq(C1(t).diff(t), -(k10 + k12)*C1(t) + k21*C2(t))
+        ode2 = Eq(C2(t).diff(t), k12*C1(t) - k21*C2(t))
+
+        system = [ode1, ode2]
+        solution = sp.dsolve(system, [C1(t), C2(t)])
+
+        result = {
+            "model": "2-compartment IV bolus",
+            "system": [latex(eq) for eq in system],
+            "solution": [latex(sol) for sol in solution],
+        }
+        print(f"PK 2-compartment system defined")
+        for sol in solution:
+            print(f"  {sol}")
+
+    return result
+```
+
+## 5. LaTeX 数式エクスポート
+
+```python
+def export_equations_latex(equations, output_file="equations.tex"):
+    """
+    記号数式を LaTeX ファイルにエクスポート。
+
+    Parameters:
+        equations: dict — {name: sympy_expr}
+        output_file: str — 出力 LaTeX パス
+    """
+    lines = [
+        r"\documentclass{article}",
+        r"\usepackage{amsmath,amssymb}",
+        r"\begin{document}",
+        "",
+    ]
+
+    for name, expr in equations.items():
+        lines.append(f"% {name}")
+        lines.append(r"\begin{equation}")
+        lines.append(f"  {latex(expr)}")
+        lines.append(r"\end{equation}")
+        lines.append("")
+
+    lines.append(r"\end{document}")
+
+    with open(output_file, "w") as f:
+        f.write("\n".join(lines))
+
+    print(f"LaTeX exported: {output_file} ({len(equations)} equations)")
+    return output_file
+```
+
+---
+
+## パイプライン出力
+
+| 出力ファイル | 説明 | 連携先スキル |
+|---|---|---|
+| `results/symbolic_solutions.json` | 記号解 (LaTeX 形式) | → latex-formatter, academic-writing |
+| `results/ode_solutions.json` | ODE 解析解 | → systems-biology, admet-pharmacokinetics |
+| `equations.tex` | LaTeX 数式集 | → latex-formatter |
+| `figures/symbolic_plot.png` | 記号解の可視化 | → publication-figures |
+
+## パイプライン統合
+
+```
+systems-biology ──→ symbolic-mathematics ──→ latex-formatter
+  (SBML/ODE)         (SymPy 解析解)         (LaTeX 変換)
+                           │
+                           ├──→ admet-pharmacokinetics (PK モデル)
+                           ├──→ bayesian-statistics (尤度導出)
+                           └──→ computational-materials (バンド理論)
+```