SQL : Meropenem IV Cohort (MIMIC-IV)

SQL scripts to establish an ICU patient cohort receiving intravenous meropenem in the MIMIC-IV database and extract covariates for machine-learning-based risk-factor analysis.

Overview

This repository provides:

• A cohort definition based on meropenem administered via IV.
• Reusable SQL for covariate extraction suitable for downstream ML and statistical modeling.
• Notes for running on either PostgreSQL (local) or Google BigQuery.

MIMIC-IV is a large, de-identified critical care database hosted on PhysioNet. Access requires credentialing and a data use agreement. (PubMed, PhysioNet)

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Data Access (MIMIC-IV)

1. Complete human-subjects/privacy training (CITI Program “Data or Specimens Only Research”). (PhysioNet)

2. Request PhysioNet credentialed access and sign the Data Use Agreement (DUA) for MIMIC-IV. (PhysioNet)

3. Choose your compute environment:

   • BigQuery (recommended for ease & scale): MIMIC-IV v3.1 is available as mimiciv_v3_1_hosp / mimiciv_v3_1_icu. (PhysioNet)
   • Local PostgreSQL: load MIMIC-IV using community scripts (see links below). (GitHub, PhysioNet)

Cite MIMIC-IV: Johnson AEW, et al. MIMIC-IV, a freely accessible electronic health record dataset. Sci Data. 2023;10(1):1. doi:10.1038/s41597-022-01899-x. (PubMed, Nature)

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Repository Structure

.
├── sql/
│   ├── sql_for_meropenem_iv_cohort.sql   # cohort + covariates
│   └── utils/                            # optional helpers (e.g., views)
├── README.md
└── LICENSE

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Cohort Definition (Summary)

• Inclusion

  • ICU stays in MIMIC-IV with documented meropenem administration via IV.
  • Index time = first IV meropenem start during the ICU stay.

• Exclusions (example; adjust as needed)

  • Age < 18 years at admission.
  • Missing key timestamps or implausible intervals.

Adapt filters to your study protocol and local IRB requirements.

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Covariates (Examples)

The script demonstrates how to join cohort rows to commonly used MIMIC tables to derive:

• Demographics & admission details
• Comorbidity summaries (e.g., Charlson)
• Severity scores (e.g., SOFA/OASIS at or prior to index)
• Vitals/labs around index window
• Organ support (e.g., ventilation) and early interventions

Exact fields and windows are configurable near the top of the SQL.

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Quick Start

Option A: BigQuery

1. Upload sql_for_meropenem_iv_cohort.sql to BigQuery Console or run via bq CLI.
2. Set project + dataset and execute the script against MIMIC-IV v3.1 (mimiciv_v3_1_hosp, mimiciv_v3_1_icu). (PhysioNet)

Option B: Local PostgreSQL

1. Load MIMIC-IV into Postgres (see community loaders). (GitHub, PhysioNet)
2. Set your search_path to the MIMIC schemas, then run:

psql 'dbname=mimic4 user=<you> options=--search_path=mimiciv' -f sql/sql_for_meropenem_iv_cohort.sql

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Reproducibility

• Versioning: Note the MIMIC-IV version and date (e.g., v3.1). Schema names/tables can change between versions. (PhysioNet)
• Determinism: Seed any stochastic steps downstream (e.g., train/val/test splits).
• Provenance: Record your SQL commit hash and BigQuery job IDs or Postgres dump checksum.

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Ethics & Compliance

• Use only for approved research purposes consistent with the MIMIC-IV DUA.
• Do not attempt re-identification.
• Follow institutional IRB/ethics guidance.

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Helpful Links

• MIMIC-IV dataset page (v3.1 / v2.2): versions, schema notes, and updates. (PhysioNet)
• PhysioNet credentialing & DUA: steps to request access. (PhysioNet)
• CITI course instructions for PhysioNet: recommended training track. (PhysioNet)
• Postgres loading examples: community loaders and scripts. (GitHub, PhysioNet)
• MIMIC-IV paper (Sci Data, 2023): canonical reference. (PubMed, Nature)

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Citation

• MIMIC-IV: Johnson AEW, et al. MIMIC-IV, a freely accessible electronic health record dataset. Sci Data. 2023;10(1):1. doi:10.1038/s41597-022-01899-x. (PubMed)

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License

This code is released under the MIT License. Note that MIMIC-IV data remain governed by the PhysioNet DUA and are not redistributed here.

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