Georgia Tech
CSE 6250
Spring 2023
William Hoynes and Peter Berryman

Based on research paper MIMIC-Extract: A Data Extraction, Preprocessing, and Representation Pipeline for MIMIC-III By Shirly Wang, Matthew B.A. McDermott, Geeticka Chauhan, Marzyeh Ghassemi, Michael C. Hughes, Tristan Naumann and Git Repo: https://github.com/MLforHealth/MIMIC_Extract

Purpose is to use original work as bases for easier downstream manipulation of MIMIC-III datasets using Physionet BigQuery Database in Scala/Spark

1. Request Editor access to the Google Cloud project found here: https://console.cloud.google.com/iam-admin/iam?project=bdh6250-380417
2. Install the Google Cloud CLI using the instructions found here: https://cloud.google.com/sdk/docs/install-sdk.
3. Run the following command from the command line:
   <path to Google Cloud CLI installation>/google-cloud-sdk/bin/gcloud auth application-default login
   
4. Choose your Google account with credentials to the project
   
5. Run the following command from the command line:
   <path to Google Cloud CLI installation>/google-cloud-sdk/bin/gcloud config set project bdh6250-380417
6. Run src/main/scala/bdh_mimic/main/Main.scala from this project.

1. Request access to the BigQuery database provided by Physionet (requires credentialed access): https://physionet.org/content/mimiciii/1.4/
2. This will give access to the database used in this pipeline named MIMIC_Extract with corresponding queries

1. Request access to the BigQuery database provided by Physionet (requires credentialed access): https://physionet.org/content/mimiciii/1.4/
2. See file Bigquery.txt for queries to create databases for use in Scala Code