diff --git a/mimic-iv/concepts/README.md b/mimic-iv/concepts/README.md index c075a2bb..b2c3bd48 100644 --- a/mimic-iv/concepts/README.md +++ b/mimic-iv/concepts/README.md @@ -1,77 +1,89 @@ # MIMIC-IV Concepts +This folder contains scripts to generate useful abstractions of raw MIMIC-IV data ("concepts"). +The scripts are written using the **BigQuery Standard SQL Dialect**. Concepts are categorized into folders if possible, otherwise they remain in the top-level directory. The [postgres](/mimic-iv/concepts_postgres) subfolder contains automatically generated PostgreSQL versions of these scripts; [see below for how these were generated](#postgresql-concepts). Concepts are categorized into folders if possible, otherwise they remain in the top-level directory. + +The concepts are organized into individual SQL scripts, with each script generating a table. The BigQuery `mimiciv_derived` dataset under `physionet-data` contains the concepts pregenerated. Access to this dataset is available to MIMIC-IV approved users: see the [cloud instructions](https://mimic.mit.edu/docs/gettingstarted/cloud/) on how to access MIMIC-IV on BigQuery (which includes the derived concepts). + +See the [top-level readme](mimic-iv/README.md) for more information about generating the concepts. + +## Concept Index + Concepts in this folder: +``` ├── comorbidity -│ └── charlson.sql +│   └── charlson.sql ├── demographics -│ ├── age.sql -│ ├── icustay_detail.sql -│ ├── icustay_hourly.sql -│ ├── icustay_times.sql -│ └── weight_durations.sql +│   ├── age.sql +│   ├── icustay_detail.sql +│   ├── icustay_hourly.sql +│   ├── icustay_times.sql +│   └── weight_durations.sql ├── firstday -│ ├── first_day_bg.sql -│ ├── first_day_bg_art.sql -│ ├── first_day_gcs.sql -│ ├── first_day_height.sql -│ ├── first_day_lab.sql -│ ├── first_day_rrt.sql -│ ├── first_day_sofa.sql -│ ├── first_day_urine_output.sql -│ ├── first_day_vitalsign.sql -│ └── first_day_weight.sql +│   ├── first_day_bg.sql +│   ├── first_day_bg_art.sql +│   ├── first_day_gcs.sql +│   ├── first_day_height.sql +│   ├── first_day_lab.sql +│   ├── first_day_rrt.sql +│   ├── first_day_sofa.sql +│   ├── first_day_urine_output.sql +│   ├── first_day_vitalsign.sql +│   └── first_day_weight.sql ├── measurement -│ ├── bg.sql -│ ├── blood_differential.sql -│ ├── cardiac_marker.sql -│ ├── chemistry.sql -│ ├── coagulation.sql -│ ├── complete_blood_count.sql -│ ├── creatinine_baseline.sql -│ ├── enzyme.sql -│ ├── gcs.sql -│ ├── height.sql -│ ├── icp.sql -│ ├── inflammation.sql -│ ├── oxygen_delivery.sql -│ ├── rhythm.sql -│ ├── urine_output.sql -│ ├── urine_output_rate.sql -│ ├── ventilator_setting.sql -│ └── vitalsign.sql +│   ├── bg.sql +│   ├── blood_differential.sql +│   ├── cardiac_marker.sql +│   ├── chemistry.sql +│   ├── coagulation.sql +│   ├── complete_blood_count.sql +│   ├── creatinine_baseline.sql +│   ├── enzyme.sql +│   ├── gcs.sql +│   ├── height.sql +│   ├── icp.sql +│   ├── inflammation.sql +│   ├── oxygen_delivery.sql +│   ├── rhythm.sql +│   ├── urine_output.sql +│   ├── urine_output_rate.sql +│   ├── ventilator_setting.sql +│   └── vitalsign.sql ├── medication -│ ├── acei.sql -│ ├── antibiotic.sql -│ ├── dobutamine.sql -│ ├── dopamine.sql -│ ├── epinephrine.sql -│ ├── milrinone.sql -│ ├── neuroblock.sql -│ ├── norepinephrine.sql -│ ├── norepinephrine_equivalent_dose.sql -│ ├── nsaid.sql -│ ├── phenylephrine.sql -│ ├── vasoactive_agent.sql -│ └── vasopressin.sql +│   ├── acei.sql +│   ├── antibiotic.sql +│   ├── arb.sql +│   ├── dobutamine.sql +│   ├── dopamine.sql +│   ├── epinephrine.sql +│   ├── milrinone.sql +│   ├── neuroblock.sql +│   ├── norepinephrine.sql +│   ├── norepinephrine_equivalent_dose.sql +│   ├── nsaid.sql +│   ├── phenylephrine.sql +│   ├── vasoactive_agent.sql +│   └── vasopressin.sql ├── organfailure -│ ├── kdigo_creatinine.sql -│ ├── kdigo_stages.sql -│ ├── kdigo_uo.sql -│ └── meld.sql +│   ├── kdigo_creatinine.sql +│   ├── kdigo_stages.sql +│   ├── kdigo_uo.sql +│   └── meld.sql ├── score -│ ├── apsiii.sql -│ ├── lods.sql -│ ├── oasis.sql -│ ├── sapsii.sql -│ ├── sirs.sql -│ └── sofa.sql +│   ├── apsiii.sql +│   ├── lods.sql +│   ├── oasis.sql +│   ├── sapsii.sql +│   ├── sirs.sql +│   └── sofa.sql ├── sepsis -│ ├── sepsis3.sql -│ └── suspicion_of_infection.sql +│   ├── sepsis3.sql +│   └── suspicion_of_infection.sql └── treatment ├── code_status.sql ├── crrt.sql ├── invasive_line.sql ├── rrt.sql - └── ventilation.sql \ No newline at end of file + └── ventilation.sql +```