MIT-LCP / MIT-LCP/physionet

Matching numeric files with ICU Admission ids using time stamp from numeric files

Open
#123 1 comment 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Dominant language
Python
Stars
82
Forks
21
Avg merge
35m
Merged PRs (30d)
1

Description

Hello Team,

I'm currently working on a project on MIMIC-III matched subset and trying to link numeric record files with ICU stays from clinical aspect.

Below is the logic I'm using to combine numeric records with ICU Stays:
Step#1: Extracting SUBJECT_ID and DateTime stamp from numeric files.
Step#2: Joining the [SUBJECT_ID, DateTime] with ICU Stays clinical file on SUBJECT_ID.
Step#3: For each row in the merged data, I'm further checking if the DateTime on file is in range of an ICUSTAY INTIME and OUTTIME. If yes, I'm retrieving those. If not, I'm not considering the row.

After completing this process, I'm ending up with 15860 files out of 22247. I'm wondering if this approach is valid or not, as nearly 7000 files are missed in this way.

Also, as per: https://archive.physionet.org/mimic2/mimic2_matching.shtml , there is a chance for some records to not find a match. So I'm a bit curious if I can validate the numeric files based on the ICUSTAYS IN and OUTTIMEs, and retrieve only those files which lie in the [INTIME, OUTTIME] interval. Could you please confirm if this approach is fine and it is acceptable to not find matches for nearly 7000 files?

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

Review the numeric files, the ICU Stays clinical file, and the ICUSTAYS INTIME and OUTTIME fields, then compare the proposed SUBJECT_ID and timestamp join with the MIMIC-II matching guidance linked in the issue. Done means documenting whether interval matching is valid and explaining the expected reasons for unmatched files.

Written by the indexing model from the issue text.

Assessment

Domain
data, databases
Issue type
Documentation
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
20/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.