mimic-iv/concepts: fix relation names

Since 8ed4060 the relation name prefix
is `mimiciv_`.

Author: schu

mimic-iv/concepts/README.md

@@ -3,7 +3,7 @@
 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 `mimic_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).
+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).
 
 * [List of the concept folders and their content](#concept-index)
 * [Generating the concept tables on BigQuery](#generating-the-concepts-on-bigquery)

mimic-iv/concepts/make_concepts.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-# This script generates the concepts in the BigQuery table mimic_derived.
+# This script generates the concepts in the BigQuery table mimiciv_derived.
 export TARGET_DATASET=mimiciv_derived
 
 # specify bigquery query command options

mimic-iv/concepts/measurement/oxygen_delivery.sql

@@ -61,7 +61,7 @@ with ce_stg1 as
         , itemid
         , value AS o2_device
     , ROW_NUMBER() OVER (PARTITION BY subject_id, charttime, itemid ORDER BY value) as rn
-    FROM mimic_icu.chartevents
+    FROM mimiciv_icu.chartevents
     WHERE itemid = 226732 -- oxygen delivery device(s)
 )
 , stg AS
@@ -95,4 +95,4 @@ SELECT
     , MAX(CASE WHEN rn = 4 THEN o2_device ELSE NULL END) AS o2_delivery_device_4
 FROM stg
 GROUP BY subject_id, charttime
-;
+;

mimic-iv/concepts/postgres/README.md

@@ -8,11 +8,11 @@ scripts are intended to be run against the MIMIC-IV data in a PostgreSQL databas
 To generate concepts, change to this directory and run `psql`. Then within psql, run:
 
 ```sql
--- NOTE: many scripts *require* you to use mimic_derived as the schema for outputting concepts
+-- NOTE: many scripts *require* you to use mimiciv_derived as the schema for outputting concepts
 -- change the search path at your peril!
-set search_path to mimic_derived, mimic_core, mimic_hosp, mimic_icu, mimic_ed;
+set search_path to mimiciv_derived, mimiciv_hosp, mimiciv_icu, mimiciv_ed;
 \i postgres-functions.sql -- only needs to be run once
 \i postgres-make-concepts.sql
 ```
 
-... or, execute the SQL files in your GUI of choice.
+... or, execute the SQL files in your GUI of choice.

mimic-iv/concepts/postgres/comorbidity/first_day_lab.sql

@@ -11,8 +11,8 @@ WITH cbc AS
     , MAX(platelet) as platelets_max
     , MIN(wbc) as wbc_min
     , MAX(wbc) as wbc_max
-    FROM mimic_icu.icustays ie
-    LEFT JOIN mimic_derived.complete_blood_count le
+    FROM mimiciv_icu.icustays ie
+    LEFT JOIN mimiciv_derived.complete_blood_count le
         ON le.subject_id = ie.subject_id
         AND le.charttime >= DATETIME_SUB(ie.intime, INTERVAL '6' HOUR)
         AND le.charttime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY)
@@ -34,8 +34,8 @@ WITH cbc AS
     , MIN(glucose) AS glucose_min, MAX(glucose) AS glucose_max
     , MIN(sodium) AS sodium_min, MAX(sodium) AS sodium_max
     , MIN(potassium) AS potassium_min, MAX(potassium) AS potassium_max
-    FROM mimic_icu.icustays ie
-    LEFT JOIN mimic_derived.chemistry le
+    FROM mimiciv_icu.icustays ie
+    LEFT JOIN mimiciv_derived.chemistry le
         ON le.subject_id = ie.subject_id
         AND le.charttime >= DATETIME_SUB(ie.intime, INTERVAL '6' HOUR)
         AND le.charttime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY)
@@ -55,8 +55,8 @@ WITH cbc AS
     , MIN(immature_granulocytes) AS immature_granulocytes_min, MAX(immature_granulocytes) AS immature_granulocytes_max
     , MIN(metamyelocytes) AS metamyelocytes_min, MAX(metamyelocytes) AS metamyelocytes_max
     , MIN(nrbc) AS nrbc_min, MAX(nrbc) AS nrbc_max
-    FROM mimic_icu.icustays ie
-    LEFT JOIN mimic_derived.blood_differential le
+    FROM mimiciv_icu.icustays ie
+    LEFT JOIN mimiciv_derived.blood_differential le
         ON le.subject_id = ie.subject_id
         AND le.charttime >= DATETIME_SUB(ie.intime, INTERVAL '6' HOUR)
         AND le.charttime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY)
@@ -72,8 +72,8 @@ WITH cbc AS
     , MIN(inr) AS inr_min, MAX(inr) AS inr_max
     , MIN(pt) AS pt_min, MAX(pt) AS pt_max
     , MIN(ptt) AS ptt_min, MAX(ptt) AS ptt_max
-    FROM mimic_icu.icustays ie
-    LEFT JOIN mimic_derived.coagulation le
+    FROM mimiciv_icu.icustays ie
+    LEFT JOIN mimiciv_derived.coagulation le
         ON le.subject_id = ie.subject_id
         AND le.charttime >= DATETIME_SUB(ie.intime, INTERVAL '6' HOUR)
         AND le.charttime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY)
@@ -95,8 +95,8 @@ WITH cbc AS
     , MIN(ck_mb) AS ck_mb_min, MAX(ck_mb) AS ck_mb_max
     , MIN(ggt) AS ggt_min, MAX(ggt) AS ggt_max
     , MIN(ld_ldh) AS ld_ldh_min, MAX(ld_ldh) AS ld_ldh_max
-    FROM mimic_icu.icustays ie
-    LEFT JOIN mimic_derived.enzyme le
+    FROM mimiciv_icu.icustays ie
+    LEFT JOIN mimiciv_derived.enzyme le
         ON le.subject_id = ie.subject_id
         AND le.charttime >= DATETIME_SUB(ie.intime, INTERVAL '6' HOUR)
         AND le.charttime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY)
@@ -153,7 +153,7 @@ ie.subject_id
 , ck_mb_min, ck_mb_max
 , ggt_min, ggt_max
 , ld_ldh_min, ld_ldh_max
-FROM mimic_icu.icustays ie
+FROM mimiciv_icu.icustays ie
 LEFT JOIN cbc
     ON ie.stay_id = cbc.stay_id
 LEFT JOIN chem
@@ -164,4 +164,4 @@ LEFT JOIN coag
     ON ie.stay_id = coag.stay_id
 LEFT JOIN enz
     ON ie.stay_id = enz.stay_id
-;
+;

mimic-iv/concepts/postgres/measurement/oxygen_delivery.sql

@@ -63,7 +63,7 @@ with ce_stg1 as
         , itemid
         , value AS o2_device
     , ROW_NUMBER() OVER (PARTITION BY subject_id, charttime, itemid ORDER BY value) as rn
-    FROM mimic_icu.chartevents
+    FROM mimiciv_icu.chartevents
     WHERE itemid = 226732 -- oxygen delivery device(s)
 )
 , stg AS
@@ -97,4 +97,4 @@ SELECT
     , MAX(CASE WHEN rn = 4 THEN o2_device ELSE NULL END) AS o2_delivery_device_4
 FROM stg
 GROUP BY subject_id, charttime
-;
+;