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MIT-LCP / mimic-code

MIMIC Code Repository: Code shared by the research community for the MIMIC family of databases
https://mimic.mit.edu
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Were the current Concepts codes compatible with MIMIC-IV V3.0? #1772

Open ningyile opened 3 months ago

ningyile commented 3 months ago

Prerequisites

Description

I've noticed that MIMIC-IV V3.0 has been released, and there has been discussion about installation codes. However, I've found that the item_id in MIMIC-IV V3.0 has significantly changed compared to MIMIC-IV V2.0 and V2.2. For example, the item_id for lymphocyte count is not entirely consistent between MIMIC-IV V3.0 and MIMIC-IV V2.2 (Figure was as shown below, in MIMIC-IV V2.2, the item_id for lymphocyte percentage were 51333, 52769, and 53152, while in MIMIC-IV V3.0, they were 51333, 52769, and 53132). This means that the current official Concepts codes might produce errors in accuracy when applied to MIMIC-IV V3.0 due to these item_id changes, even though the codes had no running errors.

Is it necessary to revise all the Concepts code involving the relevant item_id when installing Concepts for MIMIC-IV V3.0, or can the existing Concepts codes be used directly without revised? I would appreciate clarification on this matter. Thank you! @alistairewj

MIMIC-IV V3 0

PetrarcaBruto commented 2 months ago

Sorry, I cannot comment on that. What I found was only a loading error and I am not that familiar with the concepts code area to that level of detail.

alistairewj commented 2 months ago

They should be mostly compatible, we tried to minimize changes. The lab itemid changing is a bug - the source data updates lab names and what not over time, so we try to freeze the IDs so downstream users get the same itemid each release. I don't know why some itemid were successfully kept the same, while others changed, but it definitely shouldn't happen. Seems like a v3.1 is in order!