Hello,
I am a french ms2 bioinformatics student currently working on mimic iv data in the context of an internship. I need to convert it into the omop cdm and I would like to use this github repo for this process GitHub - OHDSI/MIMIC: MIMIC (Medical Information Mart for Intensive Care) is a large, single-center database comprising information relating to patients admitted to critical care units at a large tertiary care hospital. This repository contains the ETL to the OMOP CDM.. Though, I am very lost for running it. I have understood that we first have to run the vocab_refresh.conf. For this process I have downloaded the full mimic iv data and the omop vocabulary both in csv format, I even have created a google storage account but I don’t understand all the variables that need to be set up. What are the project template and dataset template I have to set up?
I just want to use the full mimic iv data… Moreover do I need to change the gs specified. I believe these ones were used by the team but I don’t know if i should replicate the files within my own bucket or not? I am sorry for all these questions but I am very confused when it comes to understanding the whole process… I would be very thankful if you could help me with these since this conversion is crucial to the following part of my project.
Sincerely,
Lilia OUADAH