Introduction
Athena (https://athena.ohdsi.org) is a portal to look up and download Standardized Vocabularies — an international standard vocabulary set for the entire OHDSI ecosystem. All concepts in OMOP CDM come from here.
This article explains how to look up concepts, understand common vocabulary, concept relationships, and the process of loading/importing vocabularies into the database.
1. Athena — Lookup interface
1.1 Access Athena
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 Basic lookup
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 Concept Details
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 Overview
| Vocabulary | Domain | Description | Standard? |
|---|---|---|---|
| SNOMED CT | Condition, Procedure, Observation | International Medical Terminology | ✅ Standard |
| RxNorm | Drugs | Medicine (US market) | ✅ Standard |
| RxNorm Extension | Drugs | International medicine (outside US) | ✅ Standard |
| LOINC | Measurement | Testing and measurement | ✅ Standard |
| ICD-10-CM | Conditions | Diagnosis (popular in Vietnam) | ❌ Source |
| ICD-9-CM | Conditions | Diagnostic (legacy) | ❌ Source |
| ATC | Drugs | Drug classification (WHO) | ❌ Classification |
| CPT4 | Procedure | Tips (USA) | ✅ Standard |
| HCPCS | Procedure, Device | Medical Services (USA) | ✅ Standard |
| UCUM | Unit | Unit of measurement | ✅ Standard |
| Gender | Gender | Gender | ✅ Standard |
| Race | Race | Race | ✅ Standard |
2.2 SNOMED CT — Most important Vocabulary
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 — Drug Hierarchy
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 — Measurement Codes
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
3. Concept Relationships
3.1 Important Relationship Types
-- 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!
4. Download and Import Vocabularies
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);
5. SOURCE_TO_CONCEPT_MAP — Custom Mapping
When the source data has its own code (not standard vocabulary):
-- 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'
);
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)
Summary
| Concept | Explanation |
|---|---|
| Athena | Web portal to look up and download Standardized Vocabularies |
| Standard Concept | Standard concepts used in analysis (SNOMED, RxNorm, LOINC) |
| Source Concept | Concept from original vocabulary (ICD-10, internal code) |
| Maps to | Relationship mapping source → standard concept |
| Concept Ancestors | Hierarchy table for finding children/grandchildren of concept |
| SNOMED CT | Standard Vocabulary for Condition & Procedure |
| RxNorm | Standard Vocabulary for Drug |
| LOINC | Standard Vocabulary for Measurement |
Next post: WhiteRabbit & Rabbit-in-a-Hat — Source Data Survey & ETL Design