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MIMIC III to OMOP


(Alexander Sivura) #1

Hi there.

I’ve just found CSV files with sample data from mimicIII on s3 bucket s3://ohdsi-sample-data . Where can I find additional information about it? Do you know if scripts for the conversion of the full MIMIC III dataset are available somewhere?

Kind regards,
Alex


(Andrew Williams) #2

Hi Alex,
There are a couple of ETLs from MIMIC to OMOP. This is the most current, I believe.

Since your post suggest that you found rather than downloaded the data from the stewards of MIMIC you should know that it’s important to follow the guidelines for getting approval to use the data if you haven’t already. It’s pretty easy.
Per their site: "Researchers are required to formally request access via a process documented on the MIMIC website. There are two key steps that must be completed before access is granted:

  • the researcher must complete a recognized course in protecting human research participants that includes Health Insurance Portability and Accountability Act (HIPAA) requirements.
  • the researcher must sign a data use agreement, which outlines appropriate data usage and security standards, and forbids efforts to identify individual patients.

Approval requires at least a week. Once an application has been approved the researcher will receive emails containing instructions for downloading the database from PhysioNetWorks, a restricted access component of PhysioNet."

Good luck with your work.


(Alexander Sivura) #3

Thanks Andrew. This information is super useful for us.


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