@nahisaho/satori 0.11.1 → 0.13.0

package/src/.github/skills/scientific-biothings-idmapping/SKILL.md

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+---
+name: scientific-biothings-idmapping
+description: |
+  BioThings API (MyGene.info, MyVariant.info, MyChem.info) を活用した
+  遺伝子・変異・化合物の横断的 ID マッピングおよびアノテーション統合スキル。
+---
+
+# Scientific BioThings ID Mapping
+
+BioThings API スイート (MyGene, MyVariant, MyChem) を活用した
+多データベース横断の ID 変換・アノテーション取得パイプラインを提供する。
+
+## When to Use
+
+- 遺伝子 ID 間の変換 (Entrez ↔ Ensembl ↔ Symbol ↔ UniProt) を行うとき
+- 変異 ID のアノテーション (ClinVar, dbSNP, CADD 等) を取得するとき
+- 化合物 ID の変換 (DrugBank ↔ ChEMBL ↔ InChIKey ↔ PubChem) を行うとき
+- バッチクエリで多数の ID を一括アノテーションするとき
+- 複数データベースのメタ情報を統合するとき
+
+---
+
+## Quick Start
+
+## 1. MyGene.info 遺伝子アノテーション
+
+```python
+import requests
+import pandas as pd
+
+MYGENE_API = "https://mygene.info/v3"
+
+
+def mygene_query(query, fields=None, species="human", size=10):
+    """
+    MyGene.info で遺伝子検索。
+
+    Parameters:
+        query: str — gene symbol, Entrez ID, or keyword
+        fields: str | None — comma-separated fields
+        species: str — "human", "mouse", etc.
+
+    ToolUniverse:
+        MyGene_query_genes(q=query, fields=fields, species=species)
+    """
+    params = {
+        "q": query,
+        "species": species,
+        "size": size,
+    }
+    if fields:
+        params["fields"] = fields
+
+    resp = requests.get(f"{MYGENE_API}/query", params=params)
+    resp.raise_for_status()
+    data = resp.json()
+
+    hits = data.get("hits", [])
+    print(f"MyGene query '{query}': {data.get('total', 0)} total, "
+          f"{len(hits)} returned")
+    return hits
+
+
+def mygene_get_gene(gene_id, fields=None):
+    """
+    MyGene.info 遺伝子詳細アノテーション取得。
+
+    ToolUniverse:
+        MyGene_get_gene_annotation(gene_id=gene_id, fields=fields)
+    """
+    params = {}
+    if fields:
+        params["fields"] = fields
+
+    resp = requests.get(f"{MYGENE_API}/gene/{gene_id}", params=params)
+    resp.raise_for_status()
+    data = resp.json()
+
+    print(f"MyGene gene {gene_id}: {data.get('symbol', '?')} "
+          f"({data.get('name', '')})")
+    return data
+
+
+def mygene_batch_query(gene_ids, fields=None, species="human"):
+    """
+    MyGene.info バッチ遺伝子アノテーション。
+
+    ToolUniverse:
+        MyGene_batch_query(ids=gene_ids, fields=fields, species=species)
+    """
+    payload = {
+        "ids": ",".join(str(g) for g in gene_ids),
+        "species": species,
+    }
+    if fields:
+        payload["fields"] = fields
+
+    resp = requests.post(f"{MYGENE_API}/gene", json=payload)
+    resp.raise_for_status()
+    data = resp.json()
+
+    print(f"MyGene batch: {len(gene_ids)} queried → {len(data)} results")
+    return data
+```
+
+## 2. MyVariant.info 変異アノテーション
+
+```python
+MYVARIANT_API = "https://myvariant.info/v1"
+
+
+def myvariant_get(variant_id, fields=None):
+    """
+    MyVariant.info 変異アノテーション取得。
+
+    Parameters:
+        variant_id: str — HGVS notation (e.g., "chr17:g.7674220C>T")
+
+    ToolUniverse:
+        MyVariant_get_variant_annotation(variant_id=variant_id, fields=fields)
+    """
+    params = {}
+    if fields:
+        params["fields"] = fields
+
+    resp = requests.get(f"{MYVARIANT_API}/variant/{variant_id}", params=params)
+    resp.raise_for_status()
+    data = resp.json()
+
+    clinvar = data.get("clinvar", {})
+    cadd = data.get("cadd", {})
+    print(f"MyVariant {variant_id}: "
+          f"ClinVar={clinvar.get('clinical_significance', 'N/A')}, "
+          f"CADD={cadd.get('phred', 'N/A')}")
+    return data
+
+
+def myvariant_query(query, fields=None, size=10):
+    """
+    MyVariant.info 変異検索。
+
+    ToolUniverse:
+        MyVariant_query_variants(q=query, fields=fields, size=size)
+    """
+    params = {"q": query, "size": size}
+    if fields:
+        params["fields"] = fields
+
+    resp = requests.get(f"{MYVARIANT_API}/query", params=params)
+    resp.raise_for_status()
+    data = resp.json()
+
+    hits = data.get("hits", [])
+    print(f"MyVariant query '{query}': {data.get('total', 0)} total")
+    return hits
+```
+
+## 3. MyChem.info 化合物アノテーション
+
+```python
+MYCHEM_API = "https://mychem.info/v1"
+
+
+def mychem_get(chem_id, fields=None):
+    """
+    MyChem.info 化合物アノテーション取得。
+
+    Parameters:
+        chem_id: str — InChIKey, DrugBank ID, ChEMBL ID, etc.
+
+    ToolUniverse:
+        MyChem_get_chemical_annotation(chem_id=chem_id, fields=fields)
+    """
+    params = {}
+    if fields:
+        params["fields"] = fields
+
+    resp = requests.get(f"{MYCHEM_API}/chem/{chem_id}", params=params)
+    resp.raise_for_status()
+    data = resp.json()
+
+    drugbank = data.get("drugbank", {})
+    print(f"MyChem {chem_id}: {drugbank.get('name', 'N/A')}")
+    return data
+
+
+def mychem_query(query, fields=None, size=10):
+    """
+    MyChem.info 化合物検索。
+
+    ToolUniverse:
+        MyChem_query_chemicals(q=query, fields=fields, size=size)
+    """
+    params = {"q": query, "size": size}
+    if fields:
+        params["fields"] = fields
+
+    resp = requests.get(f"{MYCHEM_API}/query", params=params)
+    resp.raise_for_status()
+    data = resp.json()
+
+    hits = data.get("hits", [])
+    print(f"MyChem query '{query}': {data.get('total', 0)} total")
+    return hits
+```
+
+## 4. クロスデータベース ID マッピング
+
+```python
+def cross_db_id_mapping(gene_symbol):
+    """
+    遺伝子シンボルから Entrez, Ensembl, UniProt, RefSeq を一括取得。
+
+    ToolUniverse (横断):
+        MyGene_query_genes(q=gene_symbol, fields="entrezgene,ensembl.gene,uniprot,refseq")
+    """
+    fields = "entrezgene,ensembl.gene,uniprot.Swiss-Prot,refseq.rna,symbol,name"
+    hits = mygene_query(gene_symbol, fields=fields)
+
+    results = []
+    for hit in hits:
+        ensembl = hit.get("ensembl", {})
+        if isinstance(ensembl, list):
+            ensembl = ensembl[0] if ensembl else {}
+        uniprot = hit.get("uniprot", {})
+
+        results.append({
+            "symbol": hit.get("symbol", ""),
+            "name": hit.get("name", ""),
+            "entrez_id": hit.get("entrezgene", ""),
+            "ensembl_gene": ensembl.get("gene", ""),
+            "uniprot_swissprot": uniprot.get("Swiss-Prot", ""),
+            "refseq_rna": hit.get("refseq", {}).get("rna", []),
+        })
+
+    df = pd.DataFrame(results)
+    print(f"ID mapping '{gene_symbol}': {len(df)} entries")
+    return df
+```
+
+## 5. バッチ統合アノテーション
+
+```python
+def batch_integrated_annotation(gene_symbols, include_variants=False):
+    """
+    複数遺伝子のバッチ統合アノテーション。
+
+    ToolUniverse (横断):
+        MyGene_batch_query(ids=entrez_ids, fields=fields)
+        MyVariant_query_variants(q=gene_query) [optional]
+    """
+    # Step 1: Batch gene annotation
+    all_hits = []
+    for symbol in gene_symbols:
+        hits = mygene_query(symbol, fields="entrezgene,symbol,name,summary")
+        all_hits.extend(hits[:1])  # top hit per symbol
+
+    df = pd.DataFrame(all_hits)
+    print(f"Batch annotation: {len(gene_symbols)} genes → {len(df)} results")
+    return df
+```
+
+## References
+
+### Output Files
+
+| ファイル | 形式 |
+|---|---|
+| `results/mygene_annotation.json` | JSON |
+| `results/myvariant_annotation.json` | JSON |
+| `results/mychem_annotation.json` | JSON |
+| `results/id_mapping.csv` | CSV |
+
+### 利用可能ツール
+
+| カテゴリ | 主要ツール | 用途 |
+|---|---|---|
+| BioThings | `MyGene_query_genes` | 遺伝子検索 |
+| BioThings | `MyGene_get_gene_annotation` | 遺伝子詳細 |
+| BioThings | `MyGene_batch_query` | バッチアノテーション |
+| BioThings | `MyVariant_get_variant_annotation` | 変異アノテーション |
+| BioThings | `MyVariant_query_variants` | 変異検索 |
+| BioThings | `MyChem_get_chemical_annotation` | 化合物アノテーション |
+| BioThings | `MyChem_query_chemicals` | 化合物検索 |
+
+### 参照スキル
+
+| スキル | 関連 |
+|---|---|
+| `scientific-variant-interpretation` | 変異アノテーション |
+| `scientific-gene-expression-transcriptomics` | 遺伝子発現 |
+| `scientific-drug-target-interaction` | DTI 解析 |
+| `scientific-rare-disease-genetics` | 希少疾患 |
+| `scientific-pathway-enrichment` | パスウェイ解析 |
+
+### 依存パッケージ
+
+`requests`, `pandas`

package/src/.github/skills/scientific-cancer-genomics/SKILL.md

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+---
+name: scientific-cancer-genomics
+description: |
+  がんゲノミクスポータル統合スキル。COSMIC (体細胞変異カタログ)、
+  cBioPortal (がんゲノミクスデータ解析)、DepMap (がん細胞依存性) の
+  3 大がんゲノミクスデータベースを統合した変異プロファイリング、
+  変異シグネチャー解析、遺伝子依存性 (essentiality) 評価、
+  コピー数変化・がん種横断解析パイプライン。
+  13 の ToolUniverse SMCP ツールと連携。
+---
+
+# Scientific Cancer Genomics
+
+COSMIC / cBioPortal / DepMap の 3 大がんゲノミクスポータルを統合した
+体細胞変異プロファイリング・機能解析パイプラインを提供する。
+
+## When to Use
+
+- がん関連遺伝子の体細胞変異をカタログ検索するとき
+- cBioPortal でがん種横断の遺伝子変異頻度を調べるとき
+- DepMap で遺伝子依存性 (essentiality) を評価するとき
+- 変異シグネチャー解析 (SBS/DBS/ID) を行うとき
+- コピー数変化 (CNA) のドライバー・パッセンジャー分類が必要なとき
+
+---
+
+## Quick Start
+
+## 1. COSMIC 体細胞変異検索
+
+```python
+import pandas as pd
+import numpy as np
+import requests
+
+
+def cosmic_search_mutations(gene, cancer_type=None, mutation_type=None):
+    """
+    COSMIC (Catalogue Of Somatic Mutations In Cancer) 変異検索。
+
+    Parameters:
+        gene: str — 遺伝子シンボル (e.g., "BRAF", "TP53")
+        cancer_type: str — がん種フィルタ (e.g., "melanoma")
+        mutation_type: str — 変異タイプ ("missense", "nonsense", "frameshift")
+    """
+    # ToolUniverse 経由: COSMIC_search_mutations, COSMIC_get_mutations_by_gene
+    # COSMIC API は認証が必要 (Academic 無料)
+
+    # Cancer Gene Census (CGC) チェック
+    cgc_genes = {
+        "TP53": {"role": "TSG", "tier": 1},
+        "BRAF": {"role": "oncogene", "tier": 1},
+        "KRAS": {"role": "oncogene", "tier": 1},
+        "EGFR": {"role": "oncogene", "tier": 1},
+        "PIK3CA": {"role": "oncogene", "tier": 1},
+        "BRCA1": {"role": "TSG", "tier": 1},
+        "BRCA2": {"role": "TSG", "tier": 1},
+        "ALK": {"role": "oncogene", "tier": 1},
+    }
+
+    gene_info = cgc_genes.get(gene.upper(), {})
+
+    result = {
+        "gene": gene,
+        "cgc_role": gene_info.get("role", "unknown"),
+        "cgc_tier": gene_info.get("tier", None),
+        "cancer_type_filter": cancer_type,
+        "mutation_type_filter": mutation_type,
+    }
+
+    print(f"COSMIC query: {gene} "
+          f"(CGC: {gene_info.get('role', 'N/A')}, "
+          f"Tier {gene_info.get('tier', 'N/A')})")
+    return result
+```
+
+## 2. cBioPortal がんゲノミクスデータ取得
+
+```python
+def cbioportal_query(genes, study_id=None, cancer_type=None,
+                      data_types=None):
+    """
+    cBioPortal REST API によるがんゲノミクスデータ取得。
+
+    Parameters:
+        genes: list — 遺伝子シンボルリスト
+        study_id: str — cBioPortal 研究 ID (e.g., "tcga_brca_pan_can_atlas_2018")
+        cancer_type: str — がん種 (e.g., "Breast Cancer")
+        data_types: list — ["mutations", "cna", "mrna", "methylation"]
+    """
+    base_url = "https://www.cbioportal.org/api"
+
+    if data_types is None:
+        data_types = ["mutations", "cna"]
+
+    results = {}
+
+    # 研究一覧取得
+    if study_id is None:
+        resp = requests.get(f"{base_url}/studies")
+        studies = resp.json()
+        if cancer_type:
+            studies = [s for s in studies
+                       if cancer_type.lower() in
+                       s.get("cancerType", {}).get("name", "").lower()]
+        print(f"cBioPortal: {len(studies)} studies for '{cancer_type}'")
+        results["studies"] = pd.DataFrame([{
+            "study_id": s["studyId"],
+            "name": s["name"],
+            "cancer_type": s.get("cancerType", {}).get("name", ""),
+            "sample_count": s.get("allSampleCount", 0),
+        } for s in studies[:20]])
+    else:
+        # 変異データ取得
+        if "mutations" in data_types:
+            url = f"{base_url}/molecular-profiles/{study_id}_mutations/mutations"
+            params = {"projection": "DETAILED"}
+            resp = requests.get(url, params=params)
+            if resp.status_code == 200:
+                mutations = resp.json()
+                mut_df = pd.DataFrame([{
+                    "gene": m.get("gene", {}).get("hugoGeneSymbol", ""),
+                    "mutation": m.get("proteinChange", ""),
+                    "mutation_type": m.get("mutationType", ""),
+                    "chromosome": m.get("chr", ""),
+                    "position": m.get("startPosition", ""),
+                    "allele_freq": m.get("tumorAltCount", 0) /
+                                   max(m.get("tumorRefCount", 1) +
+                                       m.get("tumorAltCount", 1), 1),
+                } for m in mutations
+                    if m.get("gene", {}).get("hugoGeneSymbol", "") in genes])
+                results["mutations"] = mut_df
+                print(f"  Mutations: {len(mut_df)} found in {genes}")
+
+    return results
+```
+
+## 3. DepMap 遺伝子依存性解析
+
+```python
+def depmap_gene_dependency(genes, cell_lineage=None):
+    """
+    DepMap (Cancer Dependency Map) 遺伝子依存性解析。
+
+    Parameters:
+        genes: list — 遺伝子シンボルリスト
+        cell_lineage: str — 細胞系統フィルタ (e.g., "Lung", "Breast")
+    """
+    # ToolUniverse 経由:
+    # DepMap_search_genes, DepMap_get_gene_dependencies
+    # DepMap_get_cell_line, DepMap_get_cell_lines, DepMap_search_cell_lines
+
+    # DepMap CRISPR (Chronos) dependency score:
+    # negative = essential (依存), ~0 = non-essential
+    # Common Essential: mean < -0.5 across 90% of lines
+    # Selective Dependency: mean < -0.5 in specific lineages
+
+    results = []
+    for gene in genes:
+        result = {
+            "gene": gene,
+            "cell_lineage": cell_lineage,
+            "query_type": "CRISPR_dependency",
+            # 実際のスコアは ToolUniverse 経由で取得
+            "interpretation": (
+                "Chronos score < 0: gene essentiality increases. "
+                "score < -0.5: likely essential in this lineage. "
+                "score ~ 0: non-essential."
+            ),
+        }
+        results.append(result)
+
+    df = pd.DataFrame(results)
+    print(f"DepMap: queried {len(genes)} genes "
+          f"(lineage: {cell_lineage or 'pan-cancer'})")
+    return df
+```
+
+## 4. 変異シグネチャー解析
+
+```python
+def mutational_signature_analysis(mutations_df, genome="GRCh38",
+                                    n_signatures=None):
+    """
+    体細胞変異シグネチャー解析 (COSMIC SBS signatures)。
+
+    Parameters:
+        mutations_df: DataFrame — columns: [chr, pos, ref, alt, sample]
+        genome: str — 参照ゲノム
+        n_signatures: int — 抽出シグネチャー数 (None=自動推定)
+    """
+    from itertools import product
+
+    # 96 トリヌクレオチドコンテキスト
+    bases = ["C", "T"]
+    contexts = []
+    for ref in bases:
+        for alt in ["A", "C", "G", "T"]:
+            if ref == alt:
+                continue
+            for five in "ACGT":
+                for three in "ACGT":
+                    contexts.append(f"{five}[{ref}>{alt}]{three}")
+
+    # サンプルごとのカタログ構築
+    samples = mutations_df["sample"].unique()
+    catalog = pd.DataFrame(0, index=contexts, columns=samples)
+
+    for _, row in mutations_df.iterrows():
+        ref = row["ref"]
+        alt = row["alt"]
+        sample = row["sample"]
+        context = row.get("trinucleotide_context", "N[N>N]N")
+        if context in catalog.index:
+            catalog.loc[context, sample] += 1
+
+    print(f"Mutation catalog: {len(contexts)} contexts, "
+          f"{len(samples)} samples, "
+          f"{catalog.sum().sum():.0f} total mutations")
+
+    # NMF 分解 (SigProfilerExtractor 代替)
+    from sklearn.decomposition import NMF
+
+    X = catalog.values.T  # samples × contexts
+    if n_signatures is None:
+        n_signatures = min(5, len(samples))
+
+    model = NMF(n_components=n_signatures, random_state=42, max_iter=1000)
+    W = model.fit_transform(X)  # exposure matrix
+    H = model.components_  # signature profiles
+
+    signatures = pd.DataFrame(H.T, index=contexts,
+                               columns=[f"SBS_{i+1}" for i in range(n_signatures)])
+    exposures = pd.DataFrame(W, index=samples,
+                              columns=[f"SBS_{i+1}" for i in range(n_signatures)])
+
+    print(f"Extracted {n_signatures} mutational signatures")
+    return signatures, exposures
+```
+
+## References
+
+### Output Files
+
+| ファイル | 形式 |
+|---|---|
+| `results/cosmic_mutations.csv` | CSV |
+| `results/cbioportal_mutations.csv` | CSV |
+| `results/depmap_dependencies.csv` | CSV |
+| `results/mutation_signatures.csv` | CSV |
+| `results/signature_exposures.csv` | CSV |
+| `figures/mutation_spectrum.png` | PNG |
+| `figures/signature_profiles.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 |
+|---|---|---|
+| COSMIC | `COSMIC_search_mutations` | 体細胞変異検索 |
+| COSMIC | `COSMIC_get_mutations_by_gene` | 遺伝子別変異取得 |
+| cBioPortal | `cBioPortal_get_cancer_studies` | がん研究一覧 |
+| cBioPortal | `cBioPortal_get_mutations` | 変異データ取得 |
+| cBioPortal | `cBioPortal_get_molecular_profiles` | 分子プロファイル |
+| cBioPortal | `cBioPortal_get_patients` | 患者データ取得 |
+| cBioPortal | `cBioPortal_get_sample_lists` | サンプルリスト |
+| cBioPortal | `cBioPortal_get_samples` | サンプル詳細 |
+| DepMap | `DepMap_get_gene_dependencies` | 遺伝子依存性スコア |
+| DepMap | `DepMap_get_cell_line` | 細胞株情報 |
+| DepMap | `DepMap_get_cell_lines` | 細胞株一覧 |
+| DepMap | `DepMap_search_cell_lines` | 細胞株検索 |
+| DepMap | `DepMap_search_genes` | 遺伝子検索 |
+
+### 参照スキル
+
+| スキル | 関連 |
+|---|---|
+| `scientific-precision-oncology` | 腫瘍プロファイル → 治療選択 |
+| `scientific-variant-interpretation` | バリアント臨床解釈 |
+| `scientific-variant-effect-prediction` | 計算病原性予測 |
+| `scientific-disease-research` | GWAS → がんリスク |
+| `scientific-drug-target-profiling` | 標的同定 → 依存性 |
+
+### 依存パッケージ
+
+`pandas`, `numpy`, `requests`, `scikit-learn`, `matplotlib`