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fix: Readme mimic-iv postgres build and concepts links (#1685)
* fix: readme mimic-iv postgres links * fix: readme mimic-iv concept postgres links --------- Co-authored-by: Alistair Johnson <[email protected]>
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| # MIMIC-IV Concepts | ||
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| 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. | ||
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| 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). | ||
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| See the [top-level readme](mimic-iv/README.md) for more information about generating the concepts. | ||
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| ## Concept Index | ||
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| Concepts in this folder: | ||
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| ``` | ||
| ├── 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 | ||
| └── ventilation.sql | ||
| ``` |