MIT-LCP / MIT-LCP/mimic-code

UCUM units?

Open
#613 1 comment 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

mimic-iii
Dominant language
Jupyter Notebook
Stars
3.4k
Forks
1.7k
PR merge metrics
No merged PRs in 30d

Description

Prerequisites
Description

Will there be UCUM units in MIMIC IV?
I realize that you try to reach a balance between presenting the raw (ie original) data vs presenting corrected (and thus more useful) data, and I assume the raw data doesn't contain UCUM units. I think a supplementary table could allow you to both present the raw data and present more useful corrected data at the same time.

For example, a table called something like 'supp_units' could have columns:
-item ID (including both d_items and d_labitems item IDs)
-raw unit (the original 'valueuom')
-UCUM unit

The composite of the item ID and raw unit columns would be unique. I'm not even sure the 'raw unit' column would be needed, but if present, you could easily add a fourth column called 'LOINC code'. As item ID:LOINC code relationship might be "one to many" (or "many to many"), the inclusion of the raw unit value would help distinguish which LOINC code to use.
And by adding a LOINC column to an auxiliary (ie non-original [raw] data) table, you can leave the raw data LOINC code in place in the d_labitems (etc) table while presenting the better LOINC code in a different table without worrying about affecting those who desire just the raw data (ie those who want to clean the data themselves).

J Allen

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

The issue names no files or tests. Start by reviewing the MIMIC IV d_items and d_labitems tables, especially their valueuom data, and compare them with the proposed item-ID, raw-unit, UCUM, and LOINC mapping. Done requires a maintainer decision on whether and how this supplementary data should be provided.

Written by the indexing model from the issue text.

Assessment

Domain
databases
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
25/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.