MIMIC-IV-3.1 don`t have the derived table?

[VICKY-TU]

I am currently extracting data from the MIMIC-IV 3.1 database on the BigQuery platform. I noticed that my BigQuery project only includes eicu_crd_demo, mimiciii_demo, mimiciv_3_1_hosp, and mimiciv_3_1_icu, however, without mimiciv_3_1_derived. How could I get it?

[AnkushJamthikar]

Hi, did you get the answer to this? I am also looking to get a derived table for MIMIC-IV-3.1. Is there a way or tutorial about how to do this.

[VICKY-TU]

I didn`t find a solution on Bigquery platform, but if the data of mimic-iv 3.1 were download , the derived tables could be generated based on the file of "mimic-code-mian".

[htrucf]

I didn`t find a solution on Bigquery platform, but if the data of mimic-iv 3.1 were download , the derived tables could be generated based on the file of "mimic-code-mian".

Hi, I couldn't find any file that creates the derived dataset in the code. Could you be more specific?

[marymlucas]

In the code in Github for MIMIC-IV there is a concepts folder. The scripts to create the derived tables are there. I also replied more specifically to your question about sofa table below.

Hope this helps.

Mary

[marymlucas]

I am able to recreate the derived tables for MIMIC-IV-3.1 using the SQL scripts in the concepts folder. I did it in BigQuery - just need to make sure that in each script you're changing the path of the source tables from physionet_data.mimiciv to physionet_data.mimiciv_3_1

[marymlucas]

Yes. You would need to first create any derived tables that are referenced in the script you're trying to run.

[htrucf]

I am able to recreate the derived tables for MIMIC-IV-3.1 using the SQL scripts in the concepts folder. I did it in BigQuery - just need to make sure that in each script you're changing the path of the source tables from physionet_data.mimiciv to physionet_data.mimiciv_3_1

Hi there, I don't really understand. The SQL scripts in the concepts folder already use the derived dataset. For example, the sepsis3.sql uses physionet-data.mimiciv_derived.sofa table. And I couldn't find any SQL file that create this sofa table. What should I do or is there anything I missed? Thank you!

[marymlucas]

Hi @htrucf
You may need to go into the different folders under the mimic-iv/concepts/ folder to find the scripts you need. For example, to create the sofa table you need the sofa.sql script under /concepts/score/

https://github.com/MIT-LCP/mimic-code/tree/main/mimic-iv/concepts/score

I don't think there's anywhere that documents the hierarchy of which scripts to run first but if I have time I will document it and share here.

Mary

[htrucf]

Hi @htrucf You may need to go into the different folders under the mimic-iv/concepts/ folder to find the scripts you need. For example, to create the sofa table you need the sofa.sql script under /concepts/score/

https://github.com/MIT-LCP/mimic-code/tree/main/mimic-iv/concepts/score

I don't think there's anywhere that documents the hierarchy of which scripts to run first but if I have time I will document it and share here.

Mary

Wow, thank you so much ☺️

[marymlucas]

In case anyone is interested I have uploaded my modified SQL files for creating the derived tables using MIMICIV 3.1, the order in which I ran them to ensure they didn't fail, and a Python script to search each script and replace my BigQuery project name with yours.

You can find all the code here: https://github.com/marymlucas/mimiciv_3_1_derived

Hope this is helpful.