レッスン 7: PostgreSQL に OMOP CDM データベースをインストールする

OHDSI および OMOP CDM — 包括的な医療データ分析

パート 3: OHDSI プラットフォームの導入

xdev.asia

はじめに

OMOP CDM データベースは、すべての標準化された医療データを保存するためのプラットフォームです。 PostgreSQL は、無料、高パフォーマンス、OHDSI ツールによる優れたサポートのおかげで、OHDSI コミュニティで最も人気のある選択肢です。

---

1. PostgreSQLの準備

1.1 PostgreSQL のインストール

# Ubuntu 24.04
sudo apt update
sudo apt install -y postgresql-16 postgresql-contrib-16

# Verify
psql --version
# psql (PostgreSQL) 16.x

# Start service
sudo systemctl start postgresql
sudo systemctl enable postgresql

1.2 データベースとユーザーの作成

# Switch sang user postgres
sudo -u postgres psql

# Tạo user cho OHDSI
CREATE USER ohdsi_admin WITH PASSWORD 'secure_password_here';
CREATE USER ohdsi_app WITH PASSWORD 'app_password_here';

# Tạo database
CREATE DATABASE ohdsi OWNER ohdsi_admin;

# Tạo schemas
\c ohdsi
CREATE SCHEMA cdm AUTHORIZATION ohdsi_admin;
CREATE SCHEMA results AUTHORIZATION ohdsi_admin;
CREATE SCHEMA temp AUTHORIZATION ohdsi_admin;

-- Grant permissions
GRANT USAGE ON SCHEMA cdm TO ohdsi_app;
GRANT SELECT ON ALL TABLES IN SCHEMA cdm TO ohdsi_app;
GRANT USAGE ON SCHEMA results TO ohdsi_app;
GRANT ALL ON ALL TABLES IN SCHEMA results TO ohdsi_app;

\q

---

2. OMOP CDM スキーマの作成

2.1 DDL スクリプトのダウンロード

# Clone OMOP CDM repository
git clone https://github.com/OHDSI/CommonDataModel.git
cd CommonDataModel

# Structure
ls inst/ddl/5.4/postgresql/
# OMOPCDM_postgresql_5.4_ddl.sql          ← Tạo tables
# OMOPCDM_postgresql_5.4_primary_keys.sql ← Primary keys
# OMOPCDM_postgresql_5.4_constraints.sql  ← Foreign keys
# OMOPCDM_postgresql_5.4_indices.sql      ← Indexes

2.2 DDL スクリプトの実行

# Tạo tables
psql -h localhost -U ohdsi_admin -d ohdsi \
  -f inst/ddl/5.4/postgresql/OMOPCDM_postgresql_5.4_ddl.sql \
  -v cdmDatabaseSchema=cdm

# Verify tables created
psql -h localhost -U ohdsi_admin -d ohdsi -c "
  SELECT table_name
  FROM information_schema.tables
  WHERE table_schema = 'cdm'
  ORDER BY table_name;
"

2.3 作成後のテーブルの一覧

cdm schema:
├── care_site
├── cdm_source
├── cohort
├── cohort_definition
├── concept
├── concept_ancestor
├── concept_class
├── concept_relationship
├── concept_synonym
├── condition_era
├── condition_occurrence
├── cost
├── death
├── device_exposure
├── domain
├── dose_era
├── drug_era
├── drug_exposure
├── drug_strength
├── episode
├── episode_event
├── fact_relationship
├── location
├── measurement
├── metadata
├── note
├── note_nlp
├── observation
├── observation_period
├── payer_plan_period
├── person
├── procedure_occurrence
├── relationship
├── source_to_concept_map
├── specimen
├── visit_detail
├── visit_occurrence
└── vocabulary

---

3. 標準化された語彙をロードする

3.1 語彙ファイルの準備

# Download từ Athena (xem Bài 3)
# Unzip vocabulary_download_xxxxx.zip
unzip vocabulary_download_xxxxx.zip -d /data/vocabularies/

ls /data/vocabularies/
# CONCEPT.csv
# CONCEPT_ANCESTOR.csv
# CONCEPT_CLASS.csv
# CONCEPT_RELATIONSHIP.csv
# CONCEPT_SYNONYM.csv
# DOMAIN.csv
# DRUG_STRENGTH.csv
# RELATIONSHIP.csv
# SOURCE_TO_CONCEPT_MAP.csv
# VOCABULARY.csv

3.2 スクリプトロードの語彙

#!/bin/bash
# load_vocabularies.sh

PGHOST=localhost
PGPORT=5432
PGDATABASE=ohdsi
PGUSER=ohdsi_admin
SCHEMA=cdm
VOCAB_DIR=/data/vocabularies

export PGPASSWORD='secure_password_here'

echo "Loading Vocabularies into ${SCHEMA} schema..."

# Thứ tự load (respect FK dependencies)
TABLES=(
  "DOMAIN"
  "VOCABULARY"
  "CONCEPT_CLASS"
  "RELATIONSHIP"
  "CONCEPT"
  "CONCEPT_SYNONYM"
  "CONCEPT_RELATIONSHIP"
  "CONCEPT_ANCESTOR"
  "DRUG_STRENGTH"
  "SOURCE_TO_CONCEPT_MAP"
)

for TABLE in "${TABLES[@]}"; do
  FILE="${VOCAB_DIR}/${TABLE}.csv"
  if [ -f "$FILE" ]; then
    echo "  Loading ${TABLE}..."
    # OMOP CSV dùng TAB separator, no quote character
    psql -h $PGHOST -p $PGPORT -d $PGDATABASE -U $PGUSER -c "
      \\COPY ${SCHEMA}.${TABLE}
      FROM '${FILE}'
      WITH (FORMAT csv, HEADER true, DELIMITER E'\\t', QUOTE E'\\b')
    "
    ROW_COUNT=$(psql -h $PGHOST -p $PGPORT -d $PGDATABASE -U $PGUSER -t -c "
      SELECT COUNT(*) FROM ${SCHEMA}.${TABLE};
    ")
    echo "    → ${ROW_COUNT} rows loaded"
  else
    echo "  SKIP ${TABLE} (file not found)"
  fi
done

echo "Vocabulary loading complete!"

3.3 推定ロード時間

Table                   Rows (approx)    Time (SSD)
──────────────────────────────────────────────────
CONCEPT                 ~7,000,000       2-5 min
CONCEPT_RELATIONSHIP    ~50,000,000      15-30 min
CONCEPT_ANCESTOR        ~80,000,000      20-40 min
CONCEPT_SYNONYM         ~5,000,000       1-3 min
DRUG_STRENGTH           ~300,000         < 1 min
Others                  < 100,000 each   < 1 min
──────────────────────────────────────────────────
Total                                    ~45-90 min

---

4. インデックスと制約を作成する

4.1 主キー

psql -h localhost -U ohdsi_admin -d ohdsi \
  -f inst/ddl/5.4/postgresql/OMOPCDM_postgresql_5.4_primary_keys.sql \
  -v cdmDatabaseSchema=cdm

4.2 インデックス (パフォーマンスにとって重要)

-- Vocabulary indexes (thiết yếu cho mọi query)
CREATE INDEX idx_concept_concept_id ON cdm.concept (concept_id);
CREATE INDEX idx_concept_vocabulary ON cdm.concept (vocabulary_id, concept_code);
CREATE INDEX idx_concept_domain ON cdm.concept (domain_id);
CREATE INDEX idx_concept_standard ON cdm.concept (standard_concept);

CREATE INDEX idx_cr_c1 ON cdm.concept_relationship (concept_id_1);
CREATE INDEX idx_cr_c2 ON cdm.concept_relationship (concept_id_2);
CREATE INDEX idx_cr_rel ON cdm.concept_relationship (relationship_id);

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

-- Clinical data indexes
CREATE INDEX idx_person_id ON cdm.person (person_id);
CREATE INDEX idx_visit_person ON cdm.visit_occurrence (person_id);
CREATE INDEX idx_visit_date ON cdm.visit_occurrence (visit_start_date);
CREATE INDEX idx_co_person ON cdm.condition_occurrence (person_id);
CREATE INDEX idx_co_concept ON cdm.condition_occurrence (condition_concept_id);
CREATE INDEX idx_de_person ON cdm.drug_exposure (person_id);
CREATE INDEX idx_de_concept ON cdm.drug_exposure (drug_concept_id);
CREATE INDEX idx_m_person ON cdm.measurement (person_id);
CREATE INDEX idx_m_concept ON cdm.measurement (measurement_concept_id);

4.3 外部キー (オプション)

# FK constraints giúp data integrity nhưng chậm ETL load
# Recommendation: Tạo FK sau khi ETL hoàn thành

psql -h localhost -U ohdsi_admin -d ohdsi \
  -f inst/ddl/5.4/postgresql/OMOPCDM_postgresql_5.4_constraints.sql \
  -v cdmDatabaseSchema=cdm

---

5. PostgreSQL のパフォーマンス チューニング

5.1 OHDSI ワークロードの構成

# postgresql.conf — tối ưu cho OMOP CDM queries

# Memory (giả sử server 64GB RAM)
shared_buffers = 16GB              # 25% of RAM
effective_cache_size = 48GB        # 75% of RAM
work_mem = 256MB                   # Cho complex joins
maintenance_work_mem = 2GB         # Cho VACUUM, CREATE INDEX

# Parallel queries (OMOP queries benefit from parallelism)
max_parallel_workers_per_gather = 4
max_parallel_workers = 8
max_worker_processes = 8
parallel_tuple_cost = 0.01
parallel_setup_cost = 100

# Planner
random_page_cost = 1.1             # SSD storage
effective_io_concurrency = 200     # SSD
default_statistics_target = 500    # Better query plans

# WAL (nếu dùng cho analytics, không phải OLTP)
wal_buffers = 64MB
checkpoint_completion_target = 0.9

# Autovacuum
autovacuum_max_workers = 3
autovacuum_vacuum_cost_limit = 400

5.2 CDM ソースのメタデータ

-- Populate CDM_SOURCE table
INSERT INTO cdm.cdm_source (
  cdm_source_name,
  cdm_source_abbreviation,
  cdm_holder,
  source_description,
  cdm_etl_reference,
  source_release_date,
  cdm_release_date,
  cdm_version,
  vocabulary_version
) VALUES (
  'Hospital XYZ Vietnam',
  'HXYZ',
  'XDev Healthcare',
  'Dữ liệu HIS bệnh viện XYZ, giai đoạn 2018-2024',
  'https://github.com/xdev/ohdsi-etl',
  '2024-12-01',
  '2025-01-15',
  'v5.4',
  'v5.0 30-AUG-2024'  -- Vocabulary version từ Athena
);

---

6. インストールの確認

-- Kiểm tra vocabulary loaded
SELECT vocabulary_id, vocabulary_name, vocabulary_version
FROM cdm.vocabulary
ORDER BY vocabulary_id;

-- Đếm concepts per vocabulary
SELECT vocabulary_id, COUNT(*) AS concept_count
FROM cdm.concept
GROUP BY vocabulary_id
ORDER BY concept_count DESC
LIMIT 15;

-- Test query: tìm concept
SELECT concept_id, concept_name, vocabulary_id, domain_id
FROM cdm.concept
WHERE concept_name ILIKE '%hypertension%'
  AND standard_concept = 'S'
  AND invalid_reason IS NULL
LIMIT 10;

---

概要

ステップ	説明
1	PostgreSQL をインストールし、データベース + スキーマ (CDM、結果、一時) を作成します。
2	OMOP CDM DDL スクリプトを実行 → ~37 のテーブルを作成
3	Athena から語彙をダウンロード → 語彙テーブルにロード
4	索引の作成 (語彙 + 臨床データ)
5	OHDSI ワークロード向けに PostgreSQL をチューニングする
6	検証: クエリ試行の概念

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