MLforHealth/MIMIC_Extract

MIMIC-Extract for MIMIC-IV

bbardakk opened this issue · 6 comments

bbardakk commented

Hi,

Do you have a plan to modify MIMIC-Extract for MIMIC-IV in a short time or do you think that MIMIC-Extract can works on MIMIC-IV with minimal modifications?

Thanks in advance.

mmcdermott commented

We do plan to modify it to work with MIMIC-IV, but don't have a definite timeline yet. We'll post any updates on this issue as the situation evolves!

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phaniparsa commented

@mmcdermott: Any updates on the timeline to support MIMIC-IV?

hildeweerts commented

As MIMIC-III is phased out, are there any updates on the timeline to support MIMIC-IV?

mmcdermott commented

Hi Folks -- apologies for the delay in updating this. Unfortunately, as of now I don't know of any concrete efforts to extend this to MIMIC-IV.

bnestor commented

Hi, MIMIC-IV is undergoing a demo for OMOP formatting (https://physionet.org/content/mimic-iv-demo-omop/0.9/). I think we should hold off until OMOP is available so that we don't need to build an extraction pipeline for each hospital/version that comes along. But open to discussion.

bnestor commented

Hi, I just pushed a MIMIC-IV extraction script to mimiciv_extract branch. It is not perfect yet. A lot of the variable limits etc, need to be addressed. That being said, it is a good start as an additional benchmark now that we have mimiciii_extract, eicu_extract, and mimiciv_extract. Existing alternatives would be pyhealth for OMOP or mimiciv: https://pyhealth.readthedocs.io/en/latest/api/datasets/pyhealth.datasets.OMOPDataset.html Gen HPF: https://github.com/hoon9405/GenHPF ESGPT: https://github.com/mmcdermott/EventStreamGPT amongst others FHIR: https://github.com/google/fhir/tree/master for MIMICIV-on-FHIR https://physionet.org/content/mimic-iv-fhir/1.0/