CDM conversion of MIMIC dataset.
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README.md
SQL-mimic-cdm.txt

README.md

MIMIC-CDM

This is an ETL implementation for OMOP CDM conversion of MIMIC II clinical demo dataset. This is a PostgreSQL-based implementation of the ETL specification designed to generate CDM v5-compatible CSV files.

This implementation is under active development and is not at all ready to be used for general purpose. We have made this public so that people can contribute to this effort. We have uploaded the SQL queries, and will appreciate your suggestions to improve the ETL implementation.

Mapping

Here we list the MIMIC II source tables that have been used to generate OMOP CDM v.5 target tables.

OMOP CDM Target Table MIMIC II Source Tables
person d_patients
death d_patients
condition_occurrence icd9
visit_occurrence icustay_days
observation_period icustay_days
procedure_occurrence procedureevents, d_codeditems
drug_exposure medevents, d_meditems
measurement d_labitems, labevents
specimen d_labitems, labevents
note noteevents
provider d_caregivers
care_site d_careunits

Source code terminologies

  • Condition: ICD-9-CM
  • Measurement: LOINC
  • Procedure: ICD9-CM procedure codes

We are using concept 0 shortcut for now, where 0 means unmapped concept. We will update the concept_ids later.

Contact

If you have any question or suggestion, please contact Md Shamsuzzoha Bayzid at shams.bayzid@gmail.com.

Written with StackEdit.