Exploring MIMIC-III Critical Care Database

The examples in this repository build on the information from the MIMIC-III: Getting Started repository.

PowerPoint slides are in the root directory in both .pptx and .pdf formats for two talks:

• KU Med Frontier's Informatics Meetup on 2019-09-26: MIMIC III: A free publicly available EHR Database for Research

• Kansas City R Users Group on 2019-02-09: Exploring MIMIMC-III Critical Care Data Using Postgres/tidyverse/dbplyr/dplyr.

Repository Directories

Let's build a data dictionary with information about fields by table and how they can be used.

The MIMIC-III database schema can be viewed online here.

Database tables

patients

• Explore the six fields in the patients table.

• Why is there a pattern in the counts of records by subject_id?

• Let's compute age at death for patients when both dob (date of birth) and dod (date of death) are defined.

• To protect patient anonymity dates were shifted. Patients originally >89 years old show up as 300 years old! This is an unusual approach.

• Database drivers RPostgres and PostgreSQL give different age-at-death density plots (for now) since date computations are not always correct.

admissions

• Explore the 15 fields in the admissions table.

• A log scale was used to view a density plot for length-of-stay computed from admit time to discharge time.

• The relationship between the diagnosis field in this table and the diagnoses_icd table information is unclear.

diagnoses_icd and d_icd_diagnoses

• Explore the diagnoses_icd fact table with additional information in the d_icd_diagnoses dimension table.

• A bar plot of seq_num (diagnosis priority) shows values can range from 1 to 39, but usually are less than 10.

• The dimension table has many icd 9 codes that are never referenced by a fact table record.

• The fact table has over 140 icd 9 codes that cannot be found in the dimension table.

• A left_join is likely more desirable than an inner_join when connecting the dimension table to the fact table.

• Computed Summaries

  • Counts by ICD Diagnosis COde

  • Counts by primary vs secondary diagnosis by ICD Diagnosis Code (stored in file)

  • Counts by 10-year age intervals by ICD Diagnosis Code (stored in file)

chartevents

• Explore chartevents table with 330 million records and over 6400 types of chart events from two different dbsources.

• Explore event categories, parameter types, and units of measure.

labevents

• The "first look" file identified data inconsistencies with valueuom (value unit of measure), and several fields in the lab items dimension.

• The file Lab-Event-Multiple-Units.xlsx identifies loinc_codes and itemids with multiple units of measure.

• The file Lab-Event-Item-Counts.xlsx shows lab event counts by loinc_code and itemid along with the label and unit(s) of measure.

• The file Lab-Event-Fluid-Category-Counts shows lab event counts by fluid (9 groups) and category (3 groups).