CodeSystem Generation

CodeSystem Generation Steps

The CodeSystem for MIMIC were generated in three steps:

1. In SQL, query and get the distinct codes for a desired codesystem
2. Add the codes to the CSV CodeSystem template
3. Generate the CodeSystem using Python code to convert the CSV template to a FHIR json CodeSystem

CodeSystem Template

The template consists of the following columns:

Column	Details	Default
code	Code that identifies a concept	Must be specified
display	Human interpretation of the code	NULL, will be dropped if empty
id	CodeSystem identifier, used for referencing
url	Canonical url for the CodeSystem	http://fhir.mimic.mimit.edu/CodeSystem/
version	Version of the CodeSystem	0.1.0
name	Captial case version of id	Drop - and capitalize words
date	Date the CodeSystem was created	Current date
publisher	Creator of the CodeSystem	SickKids
description	Short description of the CodeSystem

General Notes

• Text formatting: Need to trim any values with free text, since FHIR validator does not allow leading/trailing white spaces or double spaces.
• Template format: Most MIMIC codesystems only have a code value and no display since the additional information is not available. Just left display blank.
• Condition
  • Created CodeSystem for ICD9 and ICD10 but only one ValueSet that combines the two
• Medication
  • medication-method CodeSystem combined both the mimic_hosp.emar and mimic_icu.inputevents distinct values
  • medication-drug needs to be updated to remove duplicate prescriptions of single drugs
• Procedure
  • Created CodeSystem for ICD9 and ICD10 but only one ValueSet that combines the two