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MIT-LCP / mimic-omop

Mapping the MIMIC-III database to the OMOP schema
MIT License
128 stars 48 forks source link

creation of firstday folder #53

Open aparrot89 opened 6 years ago

aparrot89 commented 6 years ago

As did here : https://github.com/MIT-LCP/mimic-code/tree/master/concepts/firstday, this pull request introduces firstday concepts to help collaborative works on MIMIC-OMOP.

There are 3 files to create materialized views :

alistairewj commented 6 years ago

Nice - this is a good idea - I'd like your opinion on a change of approach. Initially, I wrote the first day queries, then later wrote "pivoted" queries: https://github.com/MIT-LCP/mimic-code/tree/master/concepts/pivot

Pivoted queries are essentially charttime with sensible columns like heart rate, blood pressure, temperature, etc. Tables are grouped to minimize nulls (vitals table, blood gas table, etc).

Now, we can easily see that first day data can be derived from pivoted tables. And in fact I like this approach a lot better, because you can change to 48 hours, or load the pivoted data directly into memory and use the entire time series.

What do you think?

aparrot89 commented 6 years ago

Hello Alistair, Yes that's a good idea. I'll do that for the next scores I'll calculate Thanks for your feedback

vojtechhuser commented 4 years ago

Is there a plan to merge this PR?