Mimic Omop Save
Mapping the MIMIC-III database to the OMOP schema
MIMIC-OMOP
This repository contains an Extract-Transform-Load (ETL) process for mapping the MIMIC-III database to the OMOP Common Data Model. This process involves both transforming the structure of the database (i.e. the relational schema), but also standardizing the many concepts in the MIMIC-III database to a standard vocabulary (primarily the Athena Vocabulary, which you can explore here).
DOCUMENTATION
"WHERE IS ..."
Below in the README, we provide two sections. The first section, OMOP TABLES LOADED, lists the OMOP tables which have been populated from MIMIC-III. You can use this section to figure out what data generated each OMOP TABLE. For example, we can see that the OMOP CDM table person was populated using data from the patients and admissions table in MIMIC-III.
The second section, MIMIC TABLES EQUIVALENCE, lists all the tables in MIMIC-III, and shows where the data now exists in the OMOP CDM. For example, we can see that the MIMIC-III table patients was used to populate the OMOP CDM tables person and death.
OMOP TABLES LOADED
- PERSON
- DEATH
- VISIT_OCCURRENCE
- VISIT_DETAIL
- SPECIMEN
- MEASUREMENT
- PROCEDURE_OCCURRENCE
- CONDITION_OCCURRENCE
- OBSERVATION
- DRUG_EXPOSURE
- NOTE
- NOTE_NLP
- COHORT_DEFINITION
- COHORT
- COHORT_ATTRIBUTE
- ATTRIBUTE_DEFINITION
- CARE_SITE
- PROVIDER
MIMIC TABLES EQUIVALENCE
- patients
- admissions
- transfers
-
icustays
- The ICUSTAYS table is fully derived from the transfers table
- service
- prescriptions
- inputevents_cv
- inputevents_mv
- outputevents
- labevents
- microbiologyevents
- chartevents
- drgcodes
- datetimeevents
- procedure_icd
- procedureevents_mv
- cptevents
- diagnosis_icd
- notevents
- caregivers
- callout
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