@nahisaho/satori 0.12.0 → 0.14.0

package/src/.github/skills/scientific-ebi-databases/SKILL.md

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+---
+name: scientific-ebi-databases
+description: |
+  EBI データベース群統合アクセススキル。EBI Search 横断検索、ENA Browser
+  ヌクレオチドアーカイブ、BioStudies 研究データ、dbfetch エントリ取得、
+  MetaboLights メタボロミクスリポジトリの統合パイプライン。
+---
+
+# Scientific EBI Databases
+
+EBI Search / ENA Browser / BioStudies / dbfetch / MetaboLights を統合した
+EBI データベース群アクセスパイプラインを提供する。
+
+## When to Use
+
+- EBI Search で複数データベースを横断検索するとき
+- ENA (European Nucleotide Archive) で配列データを検索するとき
+- BioStudies で研究プロジェクトデータを探すとき
+- dbfetch でエントリを一括取得するとき
+- MetaboLights でメタボロミクス実験データにアクセスするとき
+
+---
+
+## Quick Start
+
+## 1. EBI Search 横断検索
+
+```python
+import requests
+import pandas as pd
+
+EBI_SEARCH_API = "https://www.ebi.ac.uk/ebisearch/ws/rest"
+
+
+def search_ebi(query, domain="allebi", size=25, fields=None):
+    """
+    EBI Search 横断検索 — 複数 EBI データベースを一括検索。
+
+    Parameters:
+        query: str — 検索クエリ
+        domain: str — 検索ドメイン ("allebi", "uniprot", "pdb", "ena", etc.)
+        size: int — 最大取得数
+        fields: list — 返却フィールド
+
+    ToolUniverse:
+        EBI_Search_query(query=query, domain=domain)
+        EBI_Search_get_entry(domain=domain, entry_id=entry_id)
+    """
+    params = {
+        "query": query,
+        "size": size,
+        "format": "json",
+    }
+    if fields:
+        params["fields"] = ",".join(fields)
+
+    resp = requests.get(f"{EBI_SEARCH_API}/{domain}", params=params)
+    resp.raise_for_status()
+    data = resp.json()
+
+    results = []
+    for entry in data.get("entries", []):
+        row = {"id": entry.get("id", ""), "source": entry.get("source", "")}
+        for field in entry.get("fields", {}):
+            row[field] = entry["fields"][field][0] if entry["fields"][field] else ""
+        results.append(row)
+
+    df = pd.DataFrame(results)
+    total = data.get("hitCount", 0)
+    print(f"EBI Search [{domain}] '{query}': {total} total hits, {len(df)} returned")
+    return df
+```
+
+## 2. ENA (European Nucleotide Archive) 配列検索
+
+```python
+ENA_API = "https://www.ebi.ac.uk/ena/browser/api"
+
+
+def search_ena(query, result_type="sequence", limit=100):
+    """
+    ENA ヌクレオチドアーカイブ検索。
+
+    Parameters:
+        query: str — 検索クエリ or Taxon ID
+        result_type: str — "sequence", "read_run", "analysis", "study"
+        limit: int — 最大取得数
+
+    ToolUniverse:
+        ENA_search(query=query, result=result_type)
+        ENA_get_entry(accession=accession)
+    """
+    params = {
+        "query": query,
+        "result": result_type,
+        "limit": limit,
+        "format": "json",
+    }
+    resp = requests.get(f"{ENA_API}/search", params=params)
+    resp.raise_for_status()
+    data = resp.json()
+
+    df = pd.DataFrame(data) if isinstance(data, list) else pd.DataFrame()
+    print(f"ENA search '{query}' [{result_type}]: {len(df)} entries")
+    return df
+
+
+def get_ena_entry(accession, display="json"):
+    """
+    ENA アクセッション番号によるエントリ取得。
+
+    Parameters:
+        accession: str — ENA accession (e.g., "ERS000001", "ERR000001")
+    """
+    resp = requests.get(
+        f"{ENA_API}/entry/{accession}",
+        params={"display": display}
+    )
+    resp.raise_for_status()
+    print(f"ENA entry {accession}: retrieved")
+    return resp.json() if display == "json" else resp.text
+```
+
+## 3. BioStudies 研究データ検索
+
+```python
+BIOSTUDIES_API = "https://www.ebi.ac.uk/biostudies/api/v1"
+
+
+def search_biostudies(query, page_size=25):
+    """
+    BioStudies 研究プロジェクトデータ検索。
+
+    Parameters:
+        query: str — 検索クエリ
+        page_size: int — ページサイズ
+
+    ToolUniverse:
+        BioStudies_search(query=query)
+        BioStudies_get_study(accession=accession)
+    """
+    params = {"query": query, "pageSize": page_size}
+    resp = requests.get(f"{BIOSTUDIES_API}/search", params=params)
+    resp.raise_for_status()
+    data = resp.json()
+
+    results = []
+    for hit in data.get("hits", []):
+        results.append({
+            "accession": hit.get("accno", ""),
+            "title": hit.get("title", ""),
+            "author": hit.get("author", ""),
+            "release_date": hit.get("rtime", ""),
+            "type": hit.get("type", ""),
+            "files": hit.get("files", 0),
+            "links": hit.get("links", 0),
+        })
+
+    df = pd.DataFrame(results)
+    total = data.get("totalHits", 0)
+    print(f"BioStudies search '{query}': {total} total, {len(df)} returned")
+    return df
+```
+
+## 4. dbfetch エントリ一括取得
+
+```python
+DBFETCH_API = "https://www.ebi.ac.uk/Tools/dbfetch/dbfetch"
+
+
+def dbfetch(db, ids, format_type="json", style="raw"):
+    """
+    dbfetch — EBI データベースエントリ一括取得。
+
+    Parameters:
+        db: str — データベース名 (e.g., "uniprotkb", "embl", "pdb")
+        ids: list — ID リスト
+        format_type: str — 出力形式 ("json", "fasta", "xml")
+        style: str — スタイル ("raw", "html")
+
+    ToolUniverse:
+        dbfetch_get_entries(db=db, ids=ids, format=format_type)
+    """
+    ids_str = ",".join(ids) if isinstance(ids, list) else ids
+    params = {
+        "db": db,
+        "id": ids_str,
+        "format": format_type,
+        "style": style,
+    }
+    resp = requests.get(DBFETCH_API, params=params)
+    resp.raise_for_status()
+
+    print(f"dbfetch [{db}]: {len(ids) if isinstance(ids, list) else 1} entries, "
+          f"format={format_type}")
+    if format_type == "json":
+        return resp.json()
+    return resp.text
+```
+
+## 5. MetaboLights メタボロミクスリポジトリ
+
+```python
+METABOLIGHTS_API = "https://www.ebi.ac.uk/metabolights/ws"
+
+
+def search_metabolights(query):
+    """
+    MetaboLights メタボロミクス実験データ検索。
+
+    Parameters:
+        query: str — 検索クエリ (化合物名、疾患名、生物種)
+
+    ToolUniverse:
+        MetaboLights_search_studies(query=query)
+        MetaboLights_get_study(study_id=study_id)
+    """
+    resp = requests.get(
+        f"{METABOLIGHTS_API}/studies/search",
+        params={"query": query}
+    )
+    resp.raise_for_status()
+    data = resp.json()
+
+    results = []
+    for study in data.get("content", []):
+        results.append({
+            "study_id": study.get("studyIdentifier", ""),
+            "title": study.get("title", ""),
+            "organism": study.get("organism", ""),
+            "description": (study.get("description") or "")[:200],
+            "submission_date": study.get("submissionDate", ""),
+            "status": study.get("studyStatus", ""),
+        })
+
+    df = pd.DataFrame(results)
+    print(f"MetaboLights search '{query}': {len(df)} studies")
+    return df
+
+
+def get_metabolights_study(study_id):
+    """MetaboLights 個別研究取得。"""
+    resp = requests.get(f"{METABOLIGHTS_API}/studies/{study_id}")
+    resp.raise_for_status()
+    data = resp.json()
+    print(f"MetaboLights {study_id}: {data.get('title', '')[:80]}")
+    return data
+```
+
+---
+
+## 利用可能ツール
+
+| ToolUniverse カテゴリ | 主なツール |
+|---|---|
+| `ebi_search` | `EBI_Search_query`, `EBI_Search_get_entry` |
+| `ena_browser` | `ENA_search`, `ENA_get_entry` |
+| `biostudies` | `BioStudies_search`, `BioStudies_get_study` |
+| `dbfetch` | `dbfetch_get_entries` |
+| `metabolights` | `MetaboLights_search_studies`, `MetaboLights_get_study` |
+
+## パイプライン出力
+
+| 出力ファイル | 説明 | 連携先スキル |
+|---|---|---|
+| `results/ebi_search.csv` | EBI 横断検索結果 | → bioinformatics, literature-search |
+| `results/ena_sequences.fasta` | ENA 配列データ | → genome-sequence-tools, sequence-analysis |
+| `results/biostudies_metadata.json` | 研究プロジェクト情報 | → multi-omics, systematic-review |
+| `results/metabolights_study.json` | メタボロミクスデータ | → metabolomics, metabolomics-databases |
+
+## パイプライン統合
+
+```
+genome-sequence-tools ──→ ebi-databases ──→ metabolomics-databases
+  (NCBI/BLAST)           (ENA/EBI Search)   (HMDB/MetaCyc)
+                              │
+                              ├──→ bioinformatics (配列データ)
+                              ├──→ sequence-analysis (FASTA)
+                              └──→ structural-proteomics (PDBe cross-ref)
+```

package/src/.github/skills/scientific-genome-sequence-tools/SKILL.md

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+---
+name: scientific-genome-sequence-tools
+description: |
+  ゲノム配列解析総合スキル。Ensembl ゲノムブラウザ、dbSNP 変異データ、
+  BLAST 相同性検索、NCBI Nucleotide 配列取得、GDC がんゲノミクスデータの
+  統合パイプライン。
+---
+
+# Scientific Genome Sequence Tools
+
+公的ゲノムデータベース (Ensembl, dbSNP, BLAST, NCBI, GDC) を横断した
+配列検索・変異アノテーション・がんゲノミクスパイプラインを提供する。
+
+## When to Use
+
+- ゲノム配列・エクソン構造を Ensembl から取得するとき
+- rsID から変異のアレル頻度を調べるとき
+- BLAST で塩基/アミノ酸配列の相同性検索を行うとき
+- NCBI Nucleotide から配列をフェッチするとき
+- GDC がんゲノミクスデータ (体細胞変異, CNV, 発現) を取得するとき
+
+---
+
+## Quick Start
+
+## 1. dbSNP 変異情報取得
+
+```python
+import requests
+import pandas as pd
+
+
+def get_dbsnp_variant(rsid):
+    """
+    dbSNP から rsID ベースの変異情報 (アレル頻度含む) を取得。
+
+    Parameters:
+        rsid: str — e.g. "rs7412"
+
+    ToolUniverse:
+        dbsnp_get_variant_by_rsid(rsid=rsid)
+        dbsnp_get_frequencies(rsid=rsid)
+        dbsnp_search_by_gene(gene_symbol=gene_symbol)
+    """
+    url = f"https://api.ncbi.nlm.nih.gov/variation/v0/refsnp/{rsid.lstrip('rs')}"
+    resp = requests.get(url)
+    resp.raise_for_status()
+    data = resp.json()
+
+    # Extract primary info
+    info = {
+        "rsid": f"rs{data.get('refsnp_id', '')}",
+        "create_date": data.get("create_date", ""),
+        "update_date": data.get("update_date", ""),
+    }
+
+    # Allele frequencies
+    alleles = data.get("primary_snapshot_data", {}).get(
+        "allele_annotations", []
+    )
+    freq_data = []
+    for allele in alleles:
+        for freq_entry in allele.get("frequency", []):
+            freq_data.append({
+                "study": freq_entry.get("study_name", ""),
+                "allele": freq_entry.get("allele", ""),
+                "count": freq_entry.get("allele_count", 0),
+                "total": freq_entry.get("total_count", 0),
+            })
+
+    df_freq = pd.DataFrame(freq_data)
+    print(f"dbSNP {info['rsid']}: {len(df_freq)} frequency entries")
+    return info, df_freq
+```
+
+## 2. BLAST 相同性検索
+
+```python
+import time
+
+
+def blast_search(sequence, program="blastn", database="nt", max_hits=10):
+    """
+    NCBI BLAST REST API で相同性検索。
+
+    Parameters:
+        sequence: str — query sequence (nucleotide or protein)
+        program: str — "blastn", "blastp", "blastx", "tblastn"
+        database: str — "nt", "nr", "refseq_rna", etc.
+
+    ToolUniverse:
+        BLAST_nucleotide_search(sequence=sequence, database=database)
+        BLAST_protein_search(sequence=sequence, database=database)
+    """
+    put_url = "https://blast.ncbi.nlm.nih.gov/blast/Blast.cgi"
+    params = {
+        "CMD": "Put",
+        "PROGRAM": program,
+        "DATABASE": database,
+        "QUERY": sequence,
+        "FORMAT_TYPE": "JSON2",
+        "HITLIST_SIZE": max_hits,
+    }
+    resp = requests.post(put_url, data=params)
+    resp.raise_for_status()
+
+    # Extract RID
+    import re
+    rid_match = re.search(r"RID = (\S+)", resp.text)
+    if not rid_match:
+        raise ValueError("BLAST RID not found")
+    rid = rid_match.group(1)
+    print(f"BLAST submitted: RID={rid}")
+
+    # Poll for results
+    for _ in range(60):
+        time.sleep(10)
+        check = requests.get(put_url, params={
+            "CMD": "Get", "RID": rid, "FORMAT_TYPE": "JSON2"
+        })
+        if "Status=WAITING" not in check.text:
+            break
+
+    return check.json() if check.headers.get(
+        "Content-Type", ""
+    ).startswith("application/json") else check.text
+```
+
+## 3. NCBI Nucleotide 配列フェッチ
+
+```python
+def fetch_ncbi_sequence(accession, rettype="fasta"):
+    """
+    NCBI Nucleotide (E-utilities) から配列を取得。
+
+    Parameters:
+        accession: str — NCBI accession (e.g., "NM_000546.6")
+        rettype: str — "fasta", "gb", "gbwithparts"
+
+    ToolUniverse:
+        NCBI_search_nucleotide(query=query)
+        NCBI_fetch_accessions(accessions=accessions)
+        NCBI_get_sequence(accession=accession)
+    """
+    url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
+    params = {
+        "db": "nucleotide",
+        "id": accession,
+        "rettype": rettype,
+        "retmode": "text",
+    }
+    resp = requests.get(url, params=params)
+    resp.raise_for_status()
+
+    print(f"NCBI Nucleotide '{accession}': {len(resp.text)} chars ({rettype})")
+    return resp.text
+```
+
+## 4. GDC がんゲノミクスデータ
+
+```python
+def get_gdc_mutations(gene_symbol, project_id=None):
+    """
+    NCI GDC (Genomic Data Commons) から体細胞変異データを取得。
+
+    Parameters:
+        gene_symbol: str — e.g. "TP53"
+        project_id: str | None — e.g. "TCGA-BRCA"
+
+    ToolUniverse:
+        GDC_get_ssm_by_gene(gene_symbol=gene_symbol)
+        GDC_get_mutation_frequency(project_id=project_id)
+        GDC_get_gene_expression(gene_id=gene_id, project_id=project_id)
+        GDC_get_cnv_data(gene_id=gene_id)
+        GDC_list_projects()
+        GDC_search_cases(filters=filters)
+        GDC_list_files(filters=filters)
+    """
+    url = "https://api.gdc.cancer.gov/ssms"
+    filters = {
+        "op": "and",
+        "content": [
+            {"op": "in", "content": {
+                "field": "consequence.transcript.gene.symbol",
+                "value": [gene_symbol],
+            }},
+        ],
+    }
+    if project_id:
+        filters["content"].append({
+            "op": "in",
+            "content": {
+                "field": "cases.project.project_id",
+                "value": [project_id],
+            },
+        })
+
+    import json
+    params = {
+        "filters": json.dumps(filters),
+        "fields": ("ssm_id,consequence.transcript.gene.symbol,"
+                    "consequence.transcript.aa_change,"
+                    "consequence.transcript.consequence_type,"
+                    "genomic_dna_change"),
+        "size": 100,
+        "format": "json",
+    }
+    resp = requests.get(url, params=params)
+    resp.raise_for_status()
+    hits = resp.json().get("data", {}).get("hits", [])
+
+    results = []
+    for hit in hits:
+        for csq in hit.get("consequence", []):
+            tx = csq.get("transcript", {})
+            results.append({
+                "ssm_id": hit.get("ssm_id", ""),
+                "gene": tx.get("gene", {}).get("symbol", ""),
+                "aa_change": tx.get("aa_change", ""),
+                "consequence_type": tx.get("consequence_type", ""),
+                "genomic_dna_change": hit.get("genomic_dna_change", ""),
+            })
+
+    df = pd.DataFrame(results)
+    print(f"GDC SSMs '{gene_symbol}'"
+          f"{f' ({project_id})' if project_id else ''}: {len(df)} mutations")
+    return df
+```
+
+## 5. 統合ゲノム変異パイプライン
+
+```python
+def integrated_variant_pipeline(rsid, gene_symbol=None):
+    """
+    dbSNP + GDC を統合したゲノム変異解析パイプライン。
+
+    ToolUniverse (横断):
+        dbsnp_get_variant_by_rsid(rsid) → GDC_get_ssm_by_gene(gene_symbol)
+    """
+    pipeline_result = {"rsid": rsid}
+
+    # Step 1: dbSNP
+    info, freq_df = get_dbsnp_variant(rsid)
+    pipeline_result["dbsnp"] = info
+
+    # Step 2: GDC somatic mutations (if gene provided)
+    if gene_symbol:
+        gdc_df = get_gdc_mutations(gene_symbol)
+        pipeline_result["gdc_mutation_count"] = len(gdc_df)
+        pipeline_result["gdc_top_consequences"] = (
+            gdc_df["consequence_type"].value_counts().head(5).to_dict()
+            if not gdc_df.empty else {}
+        )
+
+    print(f"Integrated variant: {rsid}"
+          f" | GDC={pipeline_result.get('gdc_mutation_count', 'N/A')}")
+    return pipeline_result
+```
+
+## References
+
+### Output Files
+
+| ファイル | 形式 |
+|---|---|
+| `results/dbsnp_variant.json` | JSON |
+| `results/dbsnp_frequencies.csv` | CSV |
+| `results/blast_results.json` | JSON |
+| `results/ncbi_sequence.fasta` | FASTA |
+| `results/gdc_mutations.csv` | CSV |
+
+### 利用可能ツール
+
+| カテゴリ | 主要ツール | 用途 |
+|---|---|---|
+| dbSNP | `dbsnp_get_variant_by_rsid` | rsID 変異情報 |
+| dbSNP | `dbsnp_get_frequencies` | アレル頻度 |
+| dbSNP | `dbsnp_search_by_gene` | 遺伝子→変異 |
+| BLAST | `BLAST_nucleotide_search` | 核酸相同性検索 |
+| BLAST | `BLAST_protein_search` | タンパク質相同性検索 |
+| NCBI | `NCBI_search_nucleotide` | 配列検索 |
+| NCBI | `NCBI_fetch_accessions` | アクセッション取得 |
+| NCBI | `NCBI_get_sequence` | 配列フェッチ |
+| GDC | `GDC_get_ssm_by_gene` | 体細胞変異 |
+| GDC | `GDC_get_mutation_frequency` | 変異頻度 |
+| GDC | `GDC_get_gene_expression` | 発現データ |
+| GDC | `GDC_get_cnv_data` | CNV データ |
+| GDC | `GDC_list_projects` | プロジェクト一覧 |
+| GDC | `GDC_search_cases` | 症例検索 |
+| GDC | `GDC_list_files` | ファイル一覧 |
+
+### 参照スキル
+
+| スキル | 関連 |
+|---|---|
+| `scientific-variant-interpretation` | 変異アノテーション |
+| `scientific-population-genetics` | 集団遺伝学 |
+| `scientific-cancer-genomics` | がんゲノミクス |
+| `scientific-rare-disease-genetics` | 希少疾患遺伝学 |
+| `scientific-biothings-idmapping` | ID マッピング |
+
+### 依存パッケージ
+
+`requests`, `pandas`