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