OHDSI Home | Forums | Wiki | Github

Argos project: 2020 OMOPed MIMIC project


(Vojtech Huser) #1

This thread is to be used to document work on converting MIMIC demo (and full) data to OMOP.

Prior ETL (https://github.com/MIT-LCP/mimic-omop) has last commits from 2 years ago and will be refreshed. Physionet v1.0 release will be based on that code. If we improve the mapping, Physionet release 2 will contain those additions. For now, we will still use that GitHub repo as the one and only repo for the ETL.

Links:

Argos Google drive folder link is: https://drive.google.com/open?id=1j-x-rwuYJr2nIs5zxCW6ST_Q-vPc1tfN

Github issue for the conversion: https://github.com/MIT-LCP/mimic-omop/issues/52

This forum thread will be primary way to communicate updates.

Argos is the dog of Odysseus. It is no acronym. We just need a name for the project.


ICU data, anyone?
MIMIC2 (and possibly MIMIC3) data in OHDSI CDM format
(Vojtech Huser) #2

May20 update: 2 additional researchers from Stanford joined the team. (see central notes on Google Drive folder). Nicolas Paris plans to run extract for demo data and help that way with relase 1.0 on Physionet. Thank you for folks who volunteers to be primary person for an OMOP table. MIT Physionet team provided guidance. If you want to volunteer as technical lead (let me know; I will assume that role until we have a volunteer for that role).

We will focus on MIMIC demo data first. We will author release notes on Google Drive (central notes).

The team has 10+ members and growing. N3C even wants to help. (update pending)


t