rename mimic_* to mimiciv_*

mimic-iv/concepts/comorbidity/charlson.sql

@@ -19,7 +19,7 @@ WITH diag AS
         hadm_id
         , CASE WHEN icd_version = 9 THEN icd_code ELSE NULL END AS icd9_code
         , CASE WHEN icd_version = 10 THEN icd_code ELSE NULL END AS icd10_code
-    FROM `physionet-data.mimic_hosp.diagnoses_icd` diag
+    FROM `physionet-data.mimiciv_hosp.diagnoses_icd` diag
 )
 , com AS
 (
@@ -253,7 +253,7 @@ WITH diag AS
             SUBSTR(icd10_code, 1, 3) IN ('B20','B21','B22','B24')
             THEN 1 
             ELSE 0 END) AS aids
-    FROM `physionet-data.mimic_hosp.admissions` ad
+    FROM `physionet-data.mimiciv_hosp.admissions` ad
     LEFT JOIN diag
     ON ad.hadm_id = diag.hadm_id
     GROUP BY ad.hadm_id
@@ -268,7 +268,7 @@ WITH diag AS
     WHEN age <= 60 THEN 2
     WHEN age <= 70 THEN 3
     ELSE 4 END AS age_score
-    FROM `physionet-data.mimic_derived.age`
+    FROM `physionet-data.mimiciv_derived.age`
 )
 SELECT 
     ad.subject_id
@@ -303,7 +303,7 @@ SELECT
     + 2*paraplegia + 2*renal_disease 
     + 6*aids
     AS charlson_comorbidity_index
-FROM `physionet-data.mimic_hosp.admissions` ad
+FROM `physionet-data.mimiciv_hosp.admissions` ad
 LEFT JOIN com
 ON ad.hadm_id = com.hadm_id
 LEFT JOIN ag

mimic-iv/concepts/demographics/age.sql

@@ -22,7 +22,7 @@ SELECT
 	, pa.anchor_age
 	, pa.anchor_year
 	, DATETIME_DIFF(ad.admittime, DATETIME(pa.anchor_year, 1, 1, 0, 0, 0), YEAR) + pa.anchor_age AS age
-FROM `physionet-data.mimic_hosp.admissions` ad
-INNER JOIN `physionet-data.mimic_hosp.patients` pa
+FROM `physionet-data.mimiciv_hosp.admissions` ad
+INNER JOIN `physionet-data.mimiciv_hosp.patients` pa
 ON ad.subject_id = pa.subject_id
 ;

mimic-iv/concepts/demographics/icustay_detail.sql

@@ -24,8 +24,8 @@ SELECT ie.subject_id, ie.hadm_id, ie.stay_id
     WHEN DENSE_RANK() OVER (PARTITION BY ie.hadm_id ORDER BY ie.intime) = 1 THEN True
     ELSE False END AS first_icu_stay
 
-FROM `physionet-data.mimic_icu.icustays` ie
-INNER JOIN `physionet-data.mimic_hosp.admissions` adm
+FROM `physionet-data.mimiciv_icu.icustays` ie
+INNER JOIN `physionet-data.mimiciv_hosp.admissions` adm
     ON ie.hadm_id = adm.hadm_id
-INNER JOIN `physionet-data.mimic_hosp.patients` pat
+INNER JOIN `physionet-data.mimiciv_hosp.patients` pat
     ON ie.subject_id = pat.subject_id

mimic-iv/concepts/demographics/icustay_hourly.sql

@@ -27,7 +27,7 @@ select
   --  we allow 24 hours before ICU admission (to grab labs before admit)
   , GENERATE_ARRAY(-24, CEIL(DATETIME_DIFF(it.outtime_hr, it.intime_hr, HOUR))) as hrs
 
-  from `physionet-data.mimic_derived.icustay_times` it
+  from `physionet-data.mimiciv_derived.icustay_times` it
 )
 SELECT stay_id
 , CAST(hr AS INT64) as hr

mimic-iv/concepts/demographics/icustay_times.sql

@@ -6,7 +6,7 @@ WITH t1 AS
     select ce.stay_id
     , min(charttime) as intime_hr
     , max(charttime) as outtime_hr
-    FROM `physionet-data.mimic_icu.chartevents` ce
+    FROM `physionet-data.mimiciv_icu.chartevents` ce
     -- only look at heart rate
     where ce.itemid = 220045
     group by ce.stay_id
@@ -16,6 +16,6 @@ select
   ie.subject_id, ie.hadm_id, ie.stay_id
   , t1.intime_hr
   , t1.outtime_hr
-FROM `physionet-data.mimic_icu.icustays` ie
+FROM `physionet-data.mimiciv_icu.icustays` ie
 left join t1
   on ie.stay_id = t1.stay_id;

mimic-iv/concepts/demographics/weight_durations.sql

@@ -9,7 +9,7 @@ WITH wt_stg as
           else 'daily' end as weight_type
       -- TODO: eliminate obvious outliers if there is a reasonable weight
       , c.valuenum as weight
-    FROM `physionet-data.mimic_icu.chartevents` c
+    FROM `physionet-data.mimiciv_icu.chartevents` c
     WHERE c.valuenum IS NOT NULL
       AND c.itemid in
       (
@@ -42,7 +42,7 @@ WITH wt_stg as
       else wt_stg1.charttime end as starttime
     , wt_stg1.weight
   from wt_stg1
-  INNER JOIN `physionet-data.mimic_icu.icustays` ie
+  INNER JOIN `physionet-data.mimiciv_icu.icustays` ie
     on ie.stay_id = wt_stg1.stay_id
 )
 , wt_stg3 as
@@ -87,7 +87,7 @@ WITH wt_stg as
     , wt.starttime as endtime
     , wt.weight
     , wt.weight_type
-  from `physionet-data.mimic_icu.icustays` ie
+  from `physionet-data.mimiciv_icu.icustays` ie
   inner join
   -- the below subquery returns one row for each unique stay_id
   -- the row contains: the first starttime and the corresponding weight

mimic-iv/concepts/firstday/first_day_bg.sql

@@ -23,8 +23,8 @@ select
     , MIN(glucose) AS glucose_min, MAX(glucose) AS glucose_max
     , MIN(potassium) AS potassium_min, MAX(potassium) AS potassium_max
     , MIN(sodium) AS sodium_min, MAX(sodium) AS sodium_max
-FROM `physionet-data.mimic_icu.icustays` ie
-LEFT JOIN `physionet-data.mimic_derived.bg` bg
+FROM `physionet-data.mimiciv_icu.icustays` ie
+LEFT JOIN `physionet-data.mimiciv_derived.bg` bg
     ON ie.subject_id = bg.subject_id
     AND bg.charttime >= DATETIME_SUB(ie.intime, INTERVAL '6' HOUR)
     AND bg.charttime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY)

mimic-iv/concepts/firstday/first_day_bg_art.sql

@@ -23,8 +23,8 @@ select
     , MIN(glucose) AS glucose_min, MAX(glucose) AS glucose_max
     , MIN(potassium) AS potassium_min, MAX(potassium) AS potassium_max
     , MIN(sodium) AS sodium_min, MAX(sodium) AS sodium_max
-FROM `physionet-data.mimic_icu.icustays` ie
-LEFT JOIN `physionet-data.mimic_derived.bg` bg
+FROM `physionet-data.mimiciv_icu.icustays` ie
+LEFT JOIN `physionet-data.mimiciv_derived.bg` bg
     ON ie.subject_id = bg.subject_id
     AND bg.specimen = 'ART.'
     AND bg.charttime >= DATETIME_SUB(ie.intime, INTERVAL '6' HOUR)

mimic-iv/concepts/firstday/first_day_gcs.sql

@@ -21,7 +21,7 @@ WITH gcs_final AS
             PARTITION BY gcs.stay_id
             ORDER BY gcs.GCS
         ) as gcs_seq
-    FROM `physionet-data.mimic_derived.gcs` gcs
+    FROM `physionet-data.mimiciv_derived.gcs` gcs
 )
 SELECT
     ie.subject_id
@@ -33,7 +33,7 @@ SELECT
     , gcs_verbal
     , gcs_eyes
     , gcs_unable
-FROM `physionet-data.mimic_icu.icustays` ie
+FROM `physionet-data.mimiciv_icu.icustays` ie
 LEFT JOIN gcs_final gs
     ON ie.stay_id = gs.stay_id
     AND gs.gcs_seq = 1

mimic-iv/concepts/firstday/first_day_height.sql

@@ -9,8 +9,8 @@ WITH ce AS
     SELECT
       c.stay_id
       , AVG(valuenum) as Height_chart
-    FROM `physionet-data.mimic_icu.chartevents` c
-    INNER JOIN `physionet-data.mimic_icu.icustays` ie ON
+    FROM `physionet-data.mimiciv_icu.chartevents` c
+    INNER JOIN `physionet-data.mimiciv_icu.icustays` ie ON
         c.stay_id = ie.stay_id
         AND c.charttime BETWEEN DATETIME_SUB(ie.intime, INTERVAL '1' DAY) AND DATETIME_ADD(ie.intime, INTERVAL '1' DAY)
     WHERE c.valuenum IS NOT NULL
@@ -22,8 +22,8 @@ SELECT
     ie.subject_id
     , ie.stay_id
     , ROUND(AVG(height), 2) AS height
-FROM `physionet-data.mimic_icu.icustays` ie
-LEFT JOIN `physionet-data.mimic_derived.height` ht
+FROM `physionet-data.mimiciv_icu.icustays` ie
+LEFT JOIN `physionet-data.mimiciv_derived.height` ht
     ON ie.stay_id = ht.stay_id
     AND ht.charttime >= DATETIME_SUB(ie.intime, INTERVAL '6' HOUR)
     AND ht.charttime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY)

mimic-iv/concepts/firstday/first_day_lab.sql

@@ -10,8 +10,8 @@ WITH cbc AS
     , MAX(platelet) as platelets_max
     , MIN(wbc) as wbc_min
     , MAX(wbc) as wbc_max
-    FROM `physionet-data.mimic_icu.icustays` ie
-    LEFT JOIN `physionet-data.mimic_derived.complete_blood_count` le
+    FROM `physionet-data.mimiciv_icu.icustays` ie
+    LEFT JOIN `physionet-data.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)
@@ -33,8 +33,8 @@ 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 `physionet-data.mimic_icu.icustays` ie
-    LEFT JOIN `physionet-data.mimic_derived.chemistry` le
+    FROM `physionet-data.mimiciv_icu.icustays` ie
+    LEFT JOIN `physionet-data.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)
@@ -54,8 +54,8 @@ WITH cbc AS
     , MIN(immature_granulocytes) AS imm_granulocytes_min, MAX(immature_granulocytes) AS imm_granulocytes_max
     , MIN(metamyelocytes) AS metas_min, MAX(metamyelocytes) AS metas_max
     , MIN(nrbc) AS nrbc_min, MAX(nrbc) AS nrbc_max
-    FROM `physionet-data.mimic_icu.icustays` ie
-    LEFT JOIN `physionet-data.mimic_derived.blood_differential` le
+    FROM `physionet-data.mimiciv_icu.icustays` ie
+    LEFT JOIN `physionet-data.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)
@@ -71,8 +71,8 @@ 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 `physionet-data.mimic_icu.icustays` ie
-    LEFT JOIN `physionet-data.mimic_derived.coagulation` le
+    FROM `physionet-data.mimiciv_icu.icustays` ie
+    LEFT JOIN `physionet-data.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)
@@ -94,8 +94,8 @@ 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 `physionet-data.mimic_icu.icustays` ie
-    LEFT JOIN `physionet-data.mimic_derived.enzyme` le
+    FROM `physionet-data.mimiciv_icu.icustays` ie
+    LEFT JOIN `physionet-data.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)
@@ -152,7 +152,7 @@ ie.subject_id
 , ck_mb_min, ck_mb_max
 , ggt_min, ggt_max
 , ld_ldh_min, ld_ldh_max
-FROM `physionet-data.mimic_icu.icustays` ie
+FROM `physionet-data.mimiciv_icu.icustays` ie
 LEFT JOIN cbc
     ON ie.stay_id = cbc.stay_id
 LEFT JOIN chem

mimic-iv/concepts/firstday/first_day_rrt.sql

@@ -6,8 +6,8 @@ select
     , MAX(dialysis_present) AS dialysis_present
     , MAX(dialysis_active) AS dialysis_active
     , STRING_AGG(DISTINCT dialysis_type, ', ') AS dialysis_type
-FROM `physionet-data.mimic_icu.icustays` ie
-LEFT JOIN `physionet-data.mimic_derived.rrt` rrt
+FROM `physionet-data.mimiciv_icu.icustays` ie
+LEFT JOIN `physionet-data.mimiciv_derived.rrt` rrt
 	ON ie.stay_id = rrt.stay_id
 	AND rrt.charttime >= DATETIME_SUB(ie.intime, INTERVAL '6' HOUR)
 	AND rrt.charttime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY)

mimic-iv/concepts/firstday/first_day_sofa.sql

@@ -29,29 +29,29 @@
 with vaso_stg as
 (
   select ie.stay_id, 'norepinephrine' AS treatment, vaso_rate as rate
-  FROM `physionet-data.mimic_icu.icustays` ie
-  INNER JOIN `physionet-data.mimic_derived.norepinephrine` mv
+  FROM `physionet-data.mimiciv_icu.icustays` ie
+  INNER JOIN `physionet-data.mimiciv_derived.norepinephrine` mv
     ON ie.stay_id = mv.stay_id
     AND mv.starttime >= DATETIME_SUB(ie.intime, INTERVAL '6' HOUR)
     AND mv.starttime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY)
   UNION ALL
   select ie.stay_id, 'epinephrine' AS treatment, vaso_rate as rate
-  FROM `physionet-data.mimic_icu.icustays` ie
-  INNER JOIN `physionet-data.mimic_derived.epinephrine` mv
+  FROM `physionet-data.mimiciv_icu.icustays` ie
+  INNER JOIN `physionet-data.mimiciv_derived.epinephrine` mv
     ON ie.stay_id = mv.stay_id
     AND mv.starttime >= DATETIME_SUB(ie.intime, INTERVAL '6' HOUR)
     AND mv.starttime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY)
   UNION ALL
   select ie.stay_id, 'dobutamine' AS treatment, vaso_rate as rate
-  FROM `physionet-data.mimic_icu.icustays` ie
-  INNER JOIN `physionet-data.mimic_derived.dobutamine` mv
+  FROM `physionet-data.mimiciv_icu.icustays` ie
+  INNER JOIN `physionet-data.mimiciv_derived.dobutamine` mv
     ON ie.stay_id = mv.stay_id
     AND mv.starttime >= DATETIME_SUB(ie.intime, INTERVAL '6' HOUR)
     AND mv.starttime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY)
   UNION ALL
   select ie.stay_id, 'dopamine' AS treatment, vaso_rate as rate
-  FROM `physionet-data.mimic_icu.icustays` ie
-  INNER JOIN `physionet-data.mimic_derived.dopamine` mv
+  FROM `physionet-data.mimiciv_icu.icustays` ie
+  INNER JOIN `physionet-data.mimiciv_derived.dopamine` mv
     ON ie.stay_id = mv.stay_id
     AND mv.starttime >= DATETIME_SUB(ie.intime, INTERVAL '6' HOUR)
     AND mv.starttime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY)
@@ -64,7 +64,7 @@ with vaso_stg as
     , max(CASE WHEN treatment = 'epinephrine' THEN rate ELSE NULL END) as rate_epinephrine
     , max(CASE WHEN treatment = 'dopamine' THEN rate ELSE NULL END) as rate_dopamine
     , max(CASE WHEN treatment = 'dobutamine' THEN rate ELSE NULL END) as rate_dobutamine
-  from `physionet-data.mimic_icu.icustays` ie
+  from `physionet-data.mimiciv_icu.icustays` ie
   LEFT JOIN vaso_stg v
       ON ie.stay_id = v.stay_id
   GROUP BY ie.stay_id
@@ -75,12 +75,12 @@ with vaso_stg as
   select ie.stay_id, bg.charttime
   , bg.pao2fio2ratio
   , case when vd.stay_id is not null then 1 else 0 end as IsVent
-  from `physionet-data.mimic_icu.icustays` ie
-  LEFT JOIN `physionet-data.mimic_derived.bg` bg
+  from `physionet-data.mimiciv_icu.icustays` ie
+  LEFT JOIN `physionet-data.mimiciv_derived.bg` bg
       ON ie.subject_id = bg.subject_id
       AND bg.charttime >= DATETIME_SUB(ie.intime, INTERVAL '6' HOUR)
       AND bg.charttime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY)
-  LEFT JOIN `physionet-data.mimic_derived.ventilation` vd
+  LEFT JOIN `physionet-data.mimiciv_derived.ventilation` vd
     ON ie.stay_id = vd.stay_id
     AND bg.charttime >= vd.starttime
     AND bg.charttime <= vd.endtime
@@ -117,18 +117,18 @@ select ie.stay_id
   , uo.UrineOutput
 
   , gcs.gcs_min
-from `physionet-data.mimic_icu.icustays` ie
+from `physionet-data.mimiciv_icu.icustays` ie
 left join vaso_mv mv
   on ie.stay_id = mv.stay_id
 left join pafi2 pf
  on ie.stay_id = pf.stay_id
-left join `physionet-data.mimic_derived.first_day_vitalsign` v
+left join `physionet-data.mimiciv_derived.first_day_vitalsign` v
   on ie.stay_id = v.stay_id
-left join `physionet-data.mimic_derived.first_day_lab` l
+left join `physionet-data.mimiciv_derived.first_day_lab` l
   on ie.stay_id = l.stay_id
-left join `physionet-data.mimic_derived.first_day_urine_output` uo
+left join `physionet-data.mimiciv_derived.first_day_urine_output` uo
   on ie.stay_id = uo.stay_id
-left join `physionet-data.mimic_derived.first_day_gcs` gcs
+left join `physionet-data.mimiciv_derived.first_day_gcs` gcs
   on ie.stay_id = gcs.stay_id
 )
 , scorecalc as
@@ -217,7 +217,7 @@ select ie.subject_id, ie.hadm_id, ie.stay_id
 , cardiovascular
 , cns
 , renal
-from `physionet-data.mimic_icu.icustays` ie
+from `physionet-data.mimiciv_icu.icustays` ie
 left join scorecalc s
   on ie.stay_id = s.stay_id
 ;

mimic-iv/concepts/firstday/first_day_urine_output.sql

@@ -4,9 +4,9 @@ SELECT
   ie.subject_id
   , ie.stay_id
   , SUM(urineoutput) AS urineoutput
-FROM `physionet-data.mimic_icu.icustays` ie
+FROM `physionet-data.mimiciv_icu.icustays` ie
 -- Join to the outputevents table to get urine output
-LEFT JOIN `physionet-data.mimic_derived.urine_output` uo
+LEFT JOIN `physionet-data.mimiciv_derived.urine_output` uo
     ON ie.stay_id = uo.stay_id
     -- ensure the data occurs during the first day
     AND uo.charttime >= ie.intime

mimic-iv/concepts/firstday/first_day_vitalsign.sql

@@ -27,8 +27,8 @@ ie.subject_id
 , MIN(glucose) AS glucose_min
 , MAX(glucose) AS glucose_max
 , AVG(glucose) AS glucose_mean
-FROM `physionet-data.mimic_icu.icustays` ie
-LEFT JOIN `physionet-data.mimic_derived.vitalsign` ce
+FROM `physionet-data.mimiciv_icu.icustays` ie
+LEFT JOIN `physionet-data.mimiciv_derived.vitalsign` ce
     ON ie.stay_id = ce.stay_id
     AND ce.charttime >= DATETIME_SUB(ie.intime, INTERVAL '6' HOUR)
     AND ce.charttime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY)

mimic-iv/concepts/firstday/first_day_weight.sql

@@ -9,9 +9,9 @@ SELECT
   , AVG(ce.weight) AS weight
   , MIN(ce.weight) AS weight_min
   , MAX(ce.weight) AS weight_max
-FROM `physionet-data.mimic_icu.icustays` ie
+FROM `physionet-data.mimiciv_icu.icustays` ie
   -- admission weight
-LEFT JOIN `physionet-data.mimic_derived.weight_durations` ce
+LEFT JOIN `physionet-data.mimiciv_derived.weight_durations` ce
     ON ie.stay_id = ce.stay_id
     -- we filter to weights documented during or before the 1st day
     AND ce.starttime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY)