第 3 課：Athena — 尋找並管理標準化詞彙

OHDSI 和 OMOP CDM — 綜合醫療數據分析

第 1 部分：OHDSI 和 OMOP CDM 概述

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簡介

雅典娜 (https://athena.ohdsi.org) 是一個尋找和下載標準化詞彙的入口網站—標準化詞彙是整個 OHDSI 生態系統的國際標準詞彙集。 All concepts in OMOP CDM come from here.

本文介紹如何尋找概念、理解常用詞彙、概念關係、將詞彙載入/匯入資料庫的過程。

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1. Athena — Lookup interface

1.1 訪問雅典娜

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 基本查找

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 概念細節

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)

---

2. Primary Vocabulary in OHDSI

2.1 概述

詞彙	網域	描述	標準？
SNOMED CT	條件、程序、觀察	國際醫學術語	✅ 標準
RxNorm	藥品	醫藥（美國市場）	✅ 標準
RxNorm 擴充	藥品	國際醫學（美國境外）	✅ 標準
LOINC	測量	測試與測量	✅ 標準
ICD-10-CM	條件	診斷（越南流行）	❌ 來源
ICD-9-CM	條件	診斷（舊版）	❌ 來源
空中交通管制	藥品	藥品分類（WHO）	❌分類
CPT4	程序	提示（美國）	✅ 標準
HCPCS	程序、設備	醫療服務（美國）	✅ 標準
UCUM	單位	計量單位	✅ 標準
性別	性別	性別	✅ 標準
比賽	比賽	比賽	✅ 標準

2.2 SNOMED CT — 最重要的詞彙

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 — 藥物層次結構

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 — 測量代碼

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. 概念關係

3.1 重要的關係類型

-- 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 — Ancestor Tree

-- 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.下載並匯入詞彙

4.1 Download from Athena

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 Download file structure

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 Import into PostgreSQL

# 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 — 自訂映射

當來源資料有自己的程式碼（非標準詞彙）時：

-- 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. Tips to look up Athena effectively

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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總結

概念	說明
雅典娜	用於尋找和下載標準化詞彙的入口網站
標準理念	分析中所使用的標準概念（SNOMED、RxNorm、LOINC）
來源概念	來自原始詞彙的概念（ICD-10，內碼）
地圖到	關係圖源→標準概念
概念祖先	用來找出概念的子/孫的層次結構表
SNOMED CT	條件與程序的標準詞彙
RxNorm	藥物標準詞彙
洛因克	測量標準詞彙

下一篇文章：WhiteRabbit 和 Rabbit-in-a-Hat — 來源資料調查和 ETL 設計