mimic-iv-note

MIMIC-IV-Note

• buildmimic - Scripts to build MIMIC-IV-Note in various database systems
  • postgres - PostgreSQL (v10+)
  • duckdb - DuckDB (serverless, single-file)
  • bigquery - BigQuery schemas

MIMIC-IV-Note contains deidentified free-text clinical notes for patients in MIMIC-IV, including discharge summaries and radiology reports. It is a separate download from MIMIC-IV and is available on PhysioNet.

There are currently no derived concept scripts for MIMIC-IV-Note.

Building the database

PostgreSQL

psql -d mimiciv -f mimic-iv-note/buildmimic/postgres/create.sql
psql -d mimiciv -v ON_ERROR_STOP=1 -v mimic_data_dir=<path to mimic-iv-note>/note \
  -f mimic-iv-note/buildmimic/postgres/load_gz.sql

See the postgres README for full details.

DuckDB

cd mimic-iv-note/buildmimic/duckdb
./import_duckdb.sh <path to mimic-iv-note>

See the duckdb README for full details.