How to load data into your PgSQL?

tmux new -s mimic_iv

Password pass(optional)

cp .pgpass ~/.pgpass

Pgsql relate operations

sudo apt install postgresql-client -y

make up

Create table and load data all in one for mimic-iv

./scripts/load_mimiciv_data.sh

mimic-iii

# under the path
# mimic_automatic/mimic-iii/buildmimic/postgres

make create-user mimic datadir="/home/ec2-user/workspace/mimic_iii/" DBNAME="mimic" DBPASS="p13240!" DBHOST="127.0.0.1"
make create-user mimic-gz datadir="/home/ec2-user/workspace/mimic_iii/" DBNAME="mimic" DBPASS="p13240!" DBHOST="127.0.0.1"

tmux operation

exit

Control+b d

attach tmux

tmux a -t mimic_iv

Dump postgressql

pg_dump -U postgres -h localhost -p 5432 -d mimic -F d -j 15 -f mimic_iii.dump

Navigating this repository

This repository contains code for five databases on PhysioNet:

• MIMIC-III - critical care data for patients admitted to ICUs at the BIDMC between 2001 - 2012
• MIMIC-IV - hospital and critical care data for patients admitted to the ED or ICU between 2008 - 2019
• MIMIC-IV-ED - emergency department data for individuals attending the ED between 2011 - 2019
• MIMIC-IV Waveforms (TBD) - this dataset has yet to be published.
• MIMIC-CXR - chest x-ray imaging and deidentified free-text radiology reports for patients admitted to the ED from 2012 - 2016

The repository contains one top-level folder containing community developed code for each datasets:

• mimic-iii - build scripts for MIMIC-III, derived concepts which are available on the physionet-data.mimiciii_derived dataset on BigQuery, and tutorials.
• mimic-iv - build scripts for MIMIC-IV, derived concepts which are available on the physionet-data.mimic_derived dataset on BigQuery, and tutorials.
• mimic-iv-cxr - code for loading and analyzing both dicom (mimic-iv-cxr/dcm) and text (mimic-iv-cxr/txt) data. In order to clearly indicate that MIMIC-CXR can be linked with MIMIC-IV, we have named this folder mimic-iv-cxr, and any references to MIMIC-CXR / MIMIC-IV-CXR are interchangeable.
• mimic-iv-ed - build scripts for MIMIC-IV-ED.
• mimic-iv-waveforms - TBD

Each subfolder has a README with further detail regarding its content.

Other useful tools

• Bloatectomy (paper) - A python based package for removing duplicate text in clinical notes

• Medication categories - Python script for extracting medications from free-text notes

• MIMIC Extract (paper) - A python based package for transforming MIMIC-III data into a machine learning friendly format

• FIDDLE (paper) - A python based package for a FlexIble Data-Driven pipeLinE (FIDDLE), transforming structured EHR data into a machine learning friendly format

• tmux

Acknowledgement

If you use code or concepts available in this repository, we would be grateful if you would:

• cite the dataset(s) you use as described in the PhysioNet project page: MIMIC-III, MIMIC-IV, MIMIC-IV-ED , and/or MIMIC-CXR
• include a DOI for the code rather than a direct link to the GitHub repo, i.e. https://doi.org/10.5281/zenodo.821872
• cite the MIMIC code repository paper: The MIMIC Code Repository: enabling reproducibility in critical care research

@article{johnson2018mimic,
  title={The MIMIC Code Repository: enabling reproducibility in critical care research},
  author={Johnson, Alistair E W and Stone, David J and Celi, Leo A and Pollard, Tom J},
  journal={Journal of the American Medical Informatics Association},
  volume={25},
  number={1},
  pages={32--39},
  year={2018},
  publisher={Oxford University Press}
}

License

By committing your code to the MIMIC Code Repository you agree to release the code under the MIT License attached to the repository.