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MIMIC2 (and possibly MIMIC3) data in OHDSI CDM format

That issue has been reported here: https://github.com/OHDSI/Achilles/issues/359 and they are currently working on a fix.

Thanks. Is this specific to multi-threading or heel? I guess I’ll wait on the patch and re-install the achilles package.

No, not related to multi threading, it has something to do with (I think) heel analysis. You might be able to sidestep the error by setting the runHeel = FALSE, however, i’m not totally sure that it will avoid the error, so please forgive me if you try and it does not work.

Physionet has a new web based system and the plan is hopefully to post the converted data on that improved system. See the discussion here. (and comment there to keep the momentum going).

Does anyone know if there are any updates on sharing a complete version of mimiciii in omop on physionet?

Especially now in Covid19 times, I would very much like to work with a cdm at home, as I can’t access my organisation’s cdm. If there isn’t a version available, I will give the ETL a try.

Thankyou

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No further progress that I’m aware of. We’re part of a proposal to add ICU data to MIMIC III and complete the OMOP ETL so it can be shared in OMOP form. It would make the data available broadly in a similar manner to the current strategy used in PhysioNet. Won’t know about how that turns out till June.

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I was emailing with Nicolas Paris and Adrien Parrot about this since Aug 2019
Please send direct email (or PM) to me if you are interested in seeing OMOP shaped MIMIC3 data offered within Physionet server. We all need to join a common project. My effort to create one was denied by physionet folks as not coming from the main person who created the ETL.

https://physionet.org/projects

You can also upvote a github issue here

(the prior proposal was closed by MIT admins)

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We would be happy to share an OMOP version of MIMIC-III on PhysioNet. We have received an OMOP-related submission in the past. The main issue with this submission was that the descriptive information was inadequate. Instructions for submitting a project to PhysioNet are at: https://physionet.org/about/publish/#sharing

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Last week I received guidance from MIT how to proceed with this. This is a call for collaborators. If you want to be invited into the PhysioNet project, please email me or respond here.
see github here Use this ETL as a way to provide MIMIC in OMOP directly on the Physionet website · Issue #52 · MIT-LCP/mimic-omop · GitHub
The project in draft mode is here

and invites are like this

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Hi @Vojtech_Huser,

I am interested and am already a registered user of Physionet.

My mail id is selvasathappan36@gmail.com

This thread is very long and goes back way in time.
Please use this new thread to document the 2020 project for conversion - called Argos.

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