レッスン 3: Athena — 標準化された語彙の検索と管理

OHDSI および OMOP CDM — 包括的な医療データ分析

パート 1: OHDSI および OMOP CDM の概要

xdev.asia

はじめに

アテナ (https://athena.ohdsi.org) は、OHDSI エコシステム全体の国際標準語彙セットである標準語彙を検索およびダウンロードするためのポータルです。 OMOP CDM のすべての概念はここから来ています。

この記事では、概念を検索する方法、一般的な語彙、概念の関係を理解する方法、および語彙をデータベースにロード/インポートするプロセスについて説明します。

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1. Athena — ルックアップインターフェイス

1.1 Athena にアクセスする

URL: https://athena.ohdsi.org
Đăng ký: Tạo tài khoản miễn phí (cần cho download vocabularies)

Giao diện chính:
┌─────────────────────────────────────────────────────────┐
│  ATHENA — OHDSI Standardized Vocabularies               │
│                                                         │
│  Search: [_____________________________________] [🔍]   │
│                                                         │
│  Filters:                                               │
│  ☑ Standard Concepts Only                               │
│  Domain: [All ▼]                                        │
│  Vocabulary: [All ▼]                                    │
│  Concept Class: [All ▼]                                 │
│  Invalid Reason: [Valid Only ▼]                          │
└─────────────────────────────────────────────────────────┘

1.2 基本的な検索

Ví dụ: Tìm "Hypertension"

Kết quả:
┌────────────┬──────────────────────────────┬────────┬──────────┐
│ Concept ID │ Concept Name                  │ Domain │ Vocab    │
├────────────┼──────────────────────────────┼────────┼──────────┤
│ 320128     │ Essential hypertension        │ Condi  │ SNOMED   │ ★ Standard
│ 316866     │ Hypertensive disorder         │ Condi  │ SNOMED   │ ★ Standard
│ 45566052   │ Essential (primary) HTN       │ Condi  │ ICD10CM  │   Non-std
│ 4228112    │ Secondary hypertension        │ Condi  │ SNOMED   │ ★ Standard
└────────────┴──────────────────────────────┴────────┴──────────┘

Chú ý:
- ★ Standard = concept dùng cho phân tích (standard_concept = 'S')
- Non-std = concept nguồn, cần mapping sang standard

1.3 コンセプトの詳細

Concept ID: 320128
Name: Essential hypertension
Domain: Condition
Vocabulary: SNOMED
Concept Class: Clinical Finding
Concept Code: 59621000
Standard: Standard (S)

Relationships:
├── Maps to: Essential hypertension (320128) — chính nó
├── Is a:    Hypertensive disorder (316866) — parent
├── Has finding site: Vascular structure (4167085)
├── Mapped from:
│   ├── I10 — Essential (primary) hypertension (ICD-10-CM)
│   ├── 401.9 — Unspecified essential HTN (ICD-9-CM)
│   └── K86 — Uncomplicated hypertension (ICPC)

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2. OHDSI の主な語彙

2.1 概要

語彙	ドメイン	説明	標準？
SNOMED CT	状態、手順、観察	国際医学用語	✅ 標準
RxNorm	薬	医薬品（米国市場）	✅ 標準
RxNorm 拡張機能	薬	国際医療（米国外）	✅ 標準
ロインク	測定	試験と測定	✅ 標準
ICD-10-CM	条件	診断（ベトナムで人気）	❌ 出典
ICD-9-CM	条件	診断 (レガシー)	❌ 出典
ATC	薬	医薬品分類 (WHO)	❌ 分類
CPT4	手順	ヒント (米国)	✅ 標準
HCPCS	手順、デバイス	医療サービス (米国)	✅ 標準
UCUM	単位	測定単位	✅ 標準
性別	性別	性別	✅ 標準
レース	レース	レース	✅ 標準

2.2 SNOMED CT — 最も重要な語彙

Hierarchy SNOMED CT:

Clinical Finding
├── Disease (bệnh)
│   ├── Disorder of cardiovascular system
│   │   ├── Hypertensive disorder (316866)
│   │   │   ├── Essential hypertension (320128)
│   │   │   ├── Malignant hypertension (4133004)
│   │   │   └── Secondary hypertension (4228112)
│   │   ├── Ischemic heart disease
│   │   │   ├── Acute myocardial infarction (4329847)
│   │   │   └── Chronic ischemic heart disease (318443)
│   │   └── Heart failure (316139)
│   └── Disorder of endocrine system
│       └── Diabetes mellitus (201820)

Procedure
├── Surgical procedure
│   ├── Coronary artery bypass (4336464)
│   └── Appendectomy (4239414)
└── Diagnostic procedure
    ├── Echocardiography (4055702)
    └── Colonoscopy (4249893)

2.3 RxNorm — 薬物の階層構造

RxNorm Concept Classes (từ tổng quát → chi tiết):

Ingredient (hoạt chất)
  └── Amlodipine (1332418)

Clinical Drug Component
  └── Amlodipine 5 MG

Clinical Drug Form
  └── Amlodipine Oral Tablet

Clinical Drug (thuốc cụ thể)
  └── Amlodipine 5 MG Oral Tablet (1332419) ← phổ biến nhất

Branded Drug
  └── Norvasc 5 MG Oral Tablet

Quantified Branded Drug
  └── Norvasc 5 MG Oral Tablet [Box of 30]

2.4 LOINC — 測定コード

LOINC cho xét nghiệm phổ biến:

LOINC Code  │ Concept Name                    │ Concept ID
────────────┼─────────────────────────────────┼───────────
2345-7      │ Glucose [Mass/volume] in Serum   │ 3004410
4548-4      │ Hemoglobin A1c                   │ 3004501
2160-0      │ Creatinine in Serum              │ 3016723
33914-3     │ eGFR                             │ 46236952
718-7       │ Hemoglobin                       │ 3000963
2093-3      │ Cholesterol Total                │ 3027114
6690-2      │ WBC count                        │ 3010813

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3. 概念の関係

3.1 重要な関係タイプ

-- Maps to: Source → Standard
-- ICD-10 "I10" → SNOMED "Essential hypertension"
SELECT *
FROM concept_relationship
WHERE concept_id_1 = 45566052    -- ICD-10 I10
  AND relationship_id = 'Maps to';
-- → concept_id_2 = 320128 (SNOMED Essential HTN)

-- Is a: Child → Parent (hierarchy)
SELECT *
FROM concept_relationship
WHERE concept_id_1 = 320128      -- Essential HTN
  AND relationship_id = 'Is a';
-- → concept_id_2 = 316866 (Hypertensive disorder)

-- Mapped from: Standard ← Source (reverse)
-- Subsumes: Parent ← Child (reverse of "Is a")

3.2 CONCEPT_ANCESTOR — 祖先ツリー

-- Tìm tất cả descendants của "Hypertensive disorder" (316866)
SELECT
  ca.descendant_concept_id,
  c.concept_name,
  ca.min_levels_of_separation,
  ca.max_levels_of_separation
FROM concept_ancestor ca
JOIN concept c ON ca.descendant_concept_id = c.concept_id
WHERE ca.ancestor_concept_id = 316866
  AND c.standard_concept = 'S'
ORDER BY ca.min_levels_of_separation;

-- Kết quả: Tất cả bệnh thuộc nhóm Hypertensive
-- → Essential HTN, Malignant HTN, Renovascular HTN, ...
-- → Rất hữu ích cho Cohort Definitions trong ATLAS!

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4. 語彙のダウンロードとインポート

4.1 Athena からダウンロードする

Bước 1: Đăng nhập athena.ohdsi.org
Bước 2: Chọn tab "Download"
Bước 3: Chọn vocabularies cần thiết

Vocabularies nên chọn (cho Việt Nam):
☑ SNOMED CT         ← Bắt buộc (Condition, Procedure standard)
☑ RxNorm            ← Bắt buộc (Drug standard)
☑ RxNorm Extension  ← Thuốc ngoài thị trường Mỹ
☑ LOINC             ← Xét nghiệm
☑ ICD-10-CM         ← Chẩn đoán (mapping source)
☑ ICD-10            ← WHO version
☑ ATC               ← Phân loại thuốc WHO
☑ UCUM              ← Đơn vị đo
☑ Gender            ← Giới tính
☑ Race              ← Chủng tộc
☑ Ethnicity         ← Dân tộc
☑ Visit             ← Loại visit
☑ Type Concept      ← Nguồn dữ liệu

Lưu ý: SNOMED CT yêu cầu license (miễn phí cho nghiên cứu)
        → Click "License required", trả lời form

Bước 4: Download → ZIP file ~2GB

4.2 ダウンロードファイルの構造

vocabulary_download_xxxxx/
├── CONCEPT.csv             (~7M rows, ~1.5GB)
├── VOCABULARY.csv
├── DOMAIN.csv
├── CONCEPT_CLASS.csv
├── CONCEPT_RELATIONSHIP.csv (~50M rows, ~5GB)
├── RELATIONSHIP.csv
├── CONCEPT_SYNONYM.csv
├── CONCEPT_ANCESTOR.csv    (~80M rows, ~3GB)
├── DRUG_STRENGTH.csv
└── SOURCE_TO_CONCEPT_MAP.csv

4.3 PostgreSQL へのインポート

# Script import vocabularies vào PostgreSQL
# Giả sử schema OMOP CDM đã được tạo

export PGHOST=localhost
export PGPORT=5432
export PGDATABASE=ohdsi
export PGUSER=ohdsi_admin
export VOCAB_DIR=/path/to/vocabulary_download

# Import từng file CSV
for table in CONCEPT VOCABULARY DOMAIN CONCEPT_CLASS \
             CONCEPT_RELATIONSHIP RELATIONSHIP \
             CONCEPT_SYNONYM CONCEPT_ANCESTOR \
             DRUG_STRENGTH SOURCE_TO_CONCEPT_MAP; do

  echo "Loading $table..."
  psql -c "\COPY ${table} FROM '${VOCAB_DIR}/${table}.csv' \
    WITH (FORMAT csv, HEADER true, DELIMITER E'\t', QUOTE E'\b')"

done

# Tạo indexes (rất quan trọng cho performance!)
echo "Creating indexes..."
psql -f /path/to/omop_cdm_indexes.sql

echo "Done! Vocabularies loaded."

-- omop_cdm_indexes.sql — Indexes quan trọng
CREATE INDEX idx_concept_concept_id ON concept (concept_id);
CREATE INDEX idx_concept_code ON concept (concept_code);
CREATE INDEX idx_concept_vocab ON concept (vocabulary_id);
CREATE INDEX idx_concept_domain ON concept (domain_id);
CREATE INDEX idx_concept_class ON concept (concept_class_id);

CREATE INDEX idx_cr_concept1 ON concept_relationship (concept_id_1);
CREATE INDEX idx_cr_concept2 ON concept_relationship (concept_id_2);
CREATE INDEX idx_cr_relationship ON concept_relationship (relationship_id);

CREATE INDEX idx_ca_ancestor ON concept_ancestor (ancestor_concept_id);
CREATE INDEX idx_ca_descendant ON concept_ancestor (descendant_concept_id);

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5. SOURCE_TO_CONCEPT_MAP — カスタム マッピング

ソース データに独自のコード (標準語彙ではない) がある場合:

-- Ví dụ: Bệnh viện dùng mã nội bộ cho thuốc
-- "AMLO5" → Amlodipine 5mg Oral Tablet (RxNorm 1332419)

INSERT INTO source_to_concept_map (
  source_code,
  source_concept_id,
  source_vocabulary_id,
  target_concept_id,
  target_vocabulary_id,
  valid_start_date,
  valid_end_date
) VALUES (
  'AMLO5',
  0,                      -- Source concept chưa có trong vocabulary
  'MY_HOSPITAL_DRUG',     -- Vocabulary ID tự tạo
  1332419,                -- Amlodipine 5mg (RxNorm)
  'RxNorm',
  '2024-01-01',
  '2099-12-31'
);

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6. Athena を効果的に調べるためのヒント

1. Luôn filter "Standard Concepts Only" khi tìm concept cho phân tích
   → Non-standard concepts chỉ dùng trong ETL mapping

2. Dùng Concept ID thay vì tên khi viết SQL
   → Tên có thể thay đổi giữa các phiên bản vocabulary

3. Kiểm tra "Mapped from" để xác nhận mapping
   → ICD-10 "I10" maps to SNOMED "Essential HTN"?

4. Dùng Concept Ancestor cho cohort definitions
   → Chọn ancestor concept = tự động bao gồm descendants

5. Cập nhật vocabularies định kỳ (mỗi 6 tháng)
   → Vocabularies được update liên tục (concepts mới, mappings mới)

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概要

コンセプト	説明
アテナ	標準化された語彙を検索およびダウンロードするための Web ポータル
スタンダードコンセプト	分析で使用される標準概念 (SNOMED、RxNorm、LOINC)
ソースコンセプト	元の語彙 (ICD-10、内部コード) からの概念
	にマップします関係マッピング ソース → 標準概念
コンセプトの祖先	概念の子/孫を検索するための階層テーブル
SNOMED CT	条件と手順の標準語彙
RxNorm	薬物の標準語彙
ロインク	測定用の標準語彙

次の投稿: WhiteRabbit と Rabbit-in-a-Hat — ソース データ調査と ETL 設計