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2020 OMOPed MIMIC project

Hi Jose,
Sorry for the delay in getting back to you!
Mik has the most up to date information on your questions.
I’m very glad you are interested in using it for your classes. What classes are you teaching?

Andrew

Hi @jposada , tagging somehow didn’t work. Seeing this by chance. Same as @AntoineLamer 's reply… Sorry!
So, currently we are working with the PhysioNet team to refine the ETL and the mapping. We had found a bit of a glitch as it seems that the itemid, which we based our mappings on, seem to be shifting by new items being introduced somewhere in the middle taking over itemids of previous items… this kind of destroyed much of our mapping and we are working to fix that.
This was realized all in BigQuery, as this is PhysioNet’s preferred platform. To make this available on a different platform such as PostGreSql would be quite desirable.
The actual costs of running one ETL is not very high (I would have to reach out for exact numbers), but it might add up once you have used up your credits.
~Mik

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hi @Andrew ,

I am teaching from the OHDSI book :slight_smile:
In the following weeks we will focus on predictive models

Thank you for the answer @mik ,

So what this means in that your dev run is ok but the following runs are affected because the itemid is not the same between data source updates? and this means I should not run
the ETL for now, is that correct?

If my assumption is correct does this means the static sample of MIMIC IV OMOP-CDM(100 patients) is ok?

BQ is ok for me, I am quite familiar :wink:

Thanks a lot for such awesome work.

Hi @jposada , want to join the ongoing effort? We still meet bi-weekly and try to sort it out, then update the repository. Let me know and I will include you in the invite!

Hi @mik ,

Thank you, Please send the invite to jposada@uninorte.edu.co

Hello, Mik. My name is Byungjin Choi from South Korea.
I have great interest in the MIMIC-OMOP project
Is the working group still in progress? Can I participate too?

Can you send the invite to choi328328@ajou.ac.kr?

"Hello everyone,

I’m Sai Varshith Reddy, a graduate research assistant from the Purkayastha Lab for Health Innovation at Indiana University. Currently, we’re working on converting data from the MIMIC-IV proprietary schema to OMOP. We’ve found a GitHub repository that contains a process for this conversion within BigQuery. However, we need to perform the ETL process on our local MySQL system instead. Could you please provide guidance on the parameters and code we should use for running this process locally?

Thank you!"

I might suggest you take a look at the SQL in these scripts and transfer them to a *.sql file that you can input into MySQL. First tackle the CREATE table commands first, suppress foreign key restrictions first, add these after all the tables have been created and data inserted into your local MySQL instance. Same for indexes. Then transfer the INSERT commands table by table to *.sql files for execution.

I operate a local OMOP on MySQL for our veterinary data as well as MIMIC-IV’s Waveform Database data.

I would also advise taking snapshots as you progress so you don’t end up having to start from the beginning. Do the CREATE, take a snapshot. After each table INSERT, take a snapshot.

Hope that helps

t