This folder contains scripts to generate materialized views in a PostgreSQL database with MIMIC installed. If you do not have access to a PostgreSQL database with MIMIC, you can read more about it in the buildmimic folder.
Concepts are categorized into folders if possible, otherwise they remain in the top-level directory.
The make-concepts.sql file can be used to build all concepts in a PostgreSQL database. It uses relative paths to call the other SQL scripts, so you need to execute the script from this folder.
These scripts derive binary flags indicating the presence of various comorbidities using billing codes (ICD-9) assigned to the patient at hospital discharge.
This is an asortment of scripts intended to give the user more familiarity with the MIMIC-III database. None of these scripts generate materialized views.
Summary of patient/admission level information such as age, height, weight, etc.
The first day subfolder contains scripts used to calculate various clinical concepts on the first day of a patient's admission to the ICU, such as the highest blood pressure, lowest temperature, etc. This folder contains many useful scripts which can be adapted to capture data outside the first day.
Useful snippets of SQL implementing common functions. For example, the auroc.sql file calculates the area under the receiver operator characteristic curve (AUROC) for a set of predictions, PRED, given a set of targets, TAR. The AUROC is a useful measure of the discrimination of a set of predictions.
Scripts in flavours of SQL which are not necessarily compatible with PostgreSQL.
Definitions of sepsis, a common cause of mortality for intensive care unit patients.
Severity of illness scores which summarize the acuity of a patient's illness on admission to the intensive care unit (usually in the first 24 hours).
Start and stop times for administration of various treatments or durations of various phenomena, including: medical agents which have a vasoactive effect on a patient's circulatory system, continuous renal replacement therapy (CRRT), and mechanical ventilation.
Below are row counts generated by each script called in make-concepts.sql. Note that a table with 61532 rows likely has one row per icustay_id, and a table with 58976 likely has one row per hadm_id.
| Script name | Row count |
|---|---|
| Top level files.. | |
| code-status.sql | 61532 |
| echo-data.sql | 45794 |
| Directory 1 of 9: durations | |
| durations/ventilation-durations.sql | 38594 |
| durations/crrt-durations.sql | 5918 |
| durations/adenosine-durations.sql | 160 |
| durations/dobutamine-durations.sql | 1792 |
| durations/dopamine-durations.sql | 6524 |
| durations/epinephrine-durations.sql | 3126 |
| durations/isuprel-durations.sql | 24 |
| durations/milrinone-durations.sql | 3600 |
| durations/norepinephrine-durations.sql | 23188 |
| durations/phenylephrine-durations.sql | 33141 |
| durations/vasopressin-durations.sql | 4190 |
| durations/vasopressor-durations.sql | 38832 |
| durations/weight-durations.sql | 158140 |
| Directory 2 of 9: comorbidity | |
| comorbidity/elixhauser-ahrq-v37-with-drg.sql | 58976 |
| comorbidity/elixhauser-ahrq-v37-no-drg.sql | 58976 |
| comorbidity/elixhauser-ahrq-v37-no-drg-all-icd.sql | 58976 |
| comorbidity/elixhauser-quan.sql | 58976 |
| comorbidity/elixhauser-score-ahrq.sql | 58976 |
| comorbidity/elixhauser-score-quan.sql | 58976 |
| Directory 3 of 9: demographics | |
| demographics/HeightWeightQuery.sql | 52971 |
| demographics/icustay-detail.sql | 61051 |
| Directory 4 of 9: firstday | |
| firstday/blood-gas-first-day.sql | 243458 |
| firstday/blood-gas-first-day-arterial.sql | 171406 |
| firstday/gcs-first-day.sql | 61532 |
| firstday/height-first-day.sql | 53432 |
| firstday/labs-first-day.sql | 61532 |
| firstday/rrt-first-day.sql | 61532 |
| firstday/urine-output-first-day.sql | 53359 |
| firstday/ventilation-first-day.sql | 61532 |
| firstday/vitals-first-day.sql | 59247 |
| firstday/weight-first-day.sql | 53432 |
| Directory 5 of 9: fluid-balance | |
| fluid-balance/urine-output.sql | 3361794 |
| Directory 6 of 9: sepsis | |
| sepsis/angus.sql | 58976 |
| sepsis/martin.sql | 58976 |
| sepsis/explicit.sql | 58976 |
| Directory 7 of 9: diagnosis | |
| ccs_diagnosis_table.sql | 15079 and 13626 |
| Directory 8 of 9: organfailure | |
| organfailure/kdigo-creatinine.sql | 61532 |
| organfailure/kdigo-uo.sql | 3361827 |
| organfailure/kdigo-stages-7day.sql | 61532 |
| organfailure/kdigo-stages-48hr.sql | 61532 |
| organfailure/meld.sql | 61532 |
| Directory 9 of 9: severityscores | |
| severityscores/oasis.sql | 61532 |
| severityscores/sofa.sql | 61532 |
| severityscores/saps.sql | 61532 |
| severityscores/sapsii.sql | 61532 |
| severityscores/apsiii.sql | 61532 |
| severityscores/lods.sql | 61532 |
| severityscores/sirs.sql | 61532 |