banderlog / mimiciii-to-fhir

Repository to transform the MIMIC-III dataset into a flat hierarchy FHIR format

MIMIC-III to FHIR conversion pipeline

This repo is based on this code, which should have been accompanying this journal article.

The original code and realization are awful, incomplete, and nonworkable ( 1, 2, 3 ).

Code from this repo actually runs without crashes, even on a 16GB RAM laptop.

But all mappings are from the original repo, and I am perfectly sure, that they have errors:

• authors used some keys that are absent in MIMIC-III tables in transform_inputevents_mv() (002-kba-... notebook)
• some resources absent in FHIR documentation
• CareVue and Metavision data should be kept in a single resource
• In the transform_procedures_icd() (004-kba-... notebook) authors messed up with the "followUp" feature
• etc

I've fixed some, but I did not check every mapping due to lack of time.

Usage

• Download MIMIC-III dataset ad put it into the data folder
• Run jupyter notebooks in ascending order
• collect CSV files from data/out/ folder

TODO

• add dtypes for all pd.read_csv() to avoid dtype guessing
• make it run on the laptop with 16GB RAM
• make mimic_fhir_transformation.py runnable and actually working code or screw it and use jupyter notebooks instead
• check mappings
• convert TRANSFERS table (should be part of encounter)?
• JSON output?
• refactoring and documentation

Conversion scheme (original)

More details in the mappings folder

MIMIC-III tables	FHIR resource
patients + admissions	patient
admissions + diagnoses_icd	encounter
icustays	encounter_icustays
cptevents + cptevents	claim
noteevents	diagnosticReport
inputevents_cv + d_items	medicationDispense
inputevents_mv + d_items	medicationDispense_mv
prescriptions	medicationRequest
chartevents + d_items	observation_ce
datetimeevents + d_items	observation_dte
labevents + d_labitems	observation_le
caregivers	practitioner
procedures_icd	procedure_icd9
procedureevents_mv + d_items	procedure_mv
outputevents + d_items	specimen_oe
microbiologyevents + d_items	specimen_mbe
services	services

Following tables were not transformed or even mentioned in the code:

• CALLOUT looks like something unimportant
• DRGCODES feels like it is not part of FHIR (the full registry of code systems defined as part of FHIR)
• TRANSFERS should be in encounters? but it's values are not in FHIR value set
• D_CPT not normative yet
• D_ICD_DIAGNOSES just ICD9 codes reference table
• D_ICD_PROCEDURES just ICD9 codes reference table