Merge pull request #1468 from schu/schu/update-mimic-iv-concepts-postgres

concepts_postgres: updates (on top of `mimiciv_v2.2_updates`)

Author: alistairewj

mimic-iv/concepts/convert_bigquery_to_postgres.sh

@@ -29,6 +29,14 @@ echo "\echo 'The scripts drop views before creating them, and these notices indi
 echo "\echo '==='" >> $TARGET_PATH/postgres-make-concepts.sql
 echo "\echo ''" >> $TARGET_PATH/postgres-make-concepts.sql
 
+echo >> $TARGET_PATH/postgres-make-concepts.sql
+echo "-- Set the search_path, i.e. the location at which we generate tables." >> $TARGET_PATH/postgres-make-concepts.sql
+echo "-- postgres looks at schemas sequentially, so this will generate tables on the mimiciv_derived schema" >> $TARGET_PATH/postgres-make-concepts.sql
+echo >> $TARGET_PATH/postgres-make-concepts.sql
+echo "-- NOTE: many scripts *require* you to use mimic_derived as the schema for outputting concepts" >> $TARGET_PATH/postgres-make-concepts.sql
+echo "-- change the search path at your peril!" >> $TARGET_PATH/postgres-make-concepts.sql
+echo "SET search_path TO mimiciv_derived, mimiciv_hosp, mimiciv_icu, mimiciv_ed;" >> $TARGET_PATH/postgres-make-concepts.sql
+
 # reporting to stdout the folder being run
 echo -n "Dependencies:"
 

mimic-iv/concepts_postgres/firstday/first_day_gcs.sql

@@ -15,15 +15,25 @@ DROP TABLE IF EXISTS first_day_gcs; CREATE TABLE first_day_gcs AS
 WITH gcs_final AS
 (
     SELECT
-        gcs.*
+        ie.subject_id, ie.stay_id
+        , g.gcs
+        , g.gcs_motor
+        , g.gcs_verbal
+        , g.gcs_eyes
+        , g.gcs_unable
         -- This sorts the data by GCS
         -- rn = 1 is the the lowest total GCS value
         , ROW_NUMBER () OVER
         (
-            PARTITION BY gcs.stay_id
-            ORDER BY gcs.GCS
+            PARTITION BY g.stay_id
+            ORDER BY g.GCS
         ) as gcs_seq
-    FROM mimiciv_derived.gcs gcs
+    FROM mimiciv_icu.icustays ie
+    -- Only get data for the first 24 hours
+    LEFT JOIN mimiciv_derived.gcs g
+        ON ie.stay_id = g.stay_id
+        AND g.charttime >= DATETIME_SUB(ie.intime, INTERVAL '6' HOUR)
+        AND g.charttime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY)
 )
 SELECT
     ie.subject_id

mimic-iv/concepts_postgres/postgres-functions.sql

@@ -3,7 +3,7 @@
 --  ???(column) -> PERCENTILE_CONT(0.5) WITHIN GROUP (ORDER BY column)    (not sure how to do median in BQ)
 
 -- Set the search_path so all functions are generated on the mimiciv_derived schema
-SET search_path TO mimiciv_derived, mimiciv_core, mimiciv_hosp, mimiciv_icu, mimiciv_ed;
+SET search_path TO mimiciv_derived, mimiciv_hosp, mimiciv_icu, mimiciv_ed;
 
 CREATE OR REPLACE FUNCTION REGEXP_EXTRACT(str TEXT, pattern TEXT) RETURNS TEXT AS $$
 BEGIN

mimic-iv/concepts_postgres/postgres-make-concepts.sql

@@ -11,7 +11,7 @@
 
 -- NOTE: many scripts *require* you to use mimic_derived as the schema for outputting concepts
 -- change the search path at your peril!
-SET search_path TO mimiciv_derived, mimiciv_core, mimiciv_hosp, mimiciv_icu, mimiciv_ed;
+SET search_path TO mimiciv_derived, mimiciv_hosp, mimiciv_icu, mimiciv_ed;
 
 -- dependencies
 \i demographics/icustay_times.sql
@@ -32,7 +32,6 @@ SET search_path TO mimiciv_derived, mimiciv_core, mimiciv_hosp, mimiciv_icu, mim
 \i measurement/coagulation.sql
 \i measurement/complete_blood_count.sql
 \i measurement/creatinine_baseline.sql
-\i measurement/differential_detailed.sql
 \i measurement/enzyme.sql
 \i measurement/gcs.sql
 \i measurement/height.sql
@@ -65,8 +64,8 @@ SET search_path TO mimiciv_derived, mimiciv_core, mimiciv_hosp, mimiciv_icu, mim
 \i treatment/ventilation.sql
 
 -- firstday
-\i firstday/first_day_bg.sql
 \i firstday/first_day_bg_art.sql
+\i firstday/first_day_bg.sql
 \i firstday/first_day_gcs.sql
 \i firstday/first_day_height.sql
 \i firstday/first_day_lab.sql

mimic-iv/concepts_postgres/sepsis/suspicion_of_infection.sql

@@ -29,7 +29,13 @@ WITH ab_tbl AS
     , CAST(MAX(chartdate) AS DATE) AS chartdate
     , MAX(charttime) AS charttime
     , MAX(spec_type_desc) AS spec_type_desc
-    , max(case when org_name is not null and org_name != '' then 1 else 0 end) as PositiveCulture
+    -- identify negative cultures as NULL organism or a specific itemid saying "NEGATIVE"
+    , MAX(
+        CASE  WHEN org_name IS NOT NULL
+              AND org_itemid != 90856
+              AND org_name != ''
+        THEN 1 ELSE 0
+      END) as PositiveCulture
   from mimiciv_hosp.microbiologyevents
   group by micro_specimen_id
 )