Merge pull request #1789 from MIT-LCP/alistair/add_arb

Add ARB
MIT-LCP · Aug 26, 2024 · 87da679 · 87da679
2 parents 781f8db + 6cc099b
commit 87da679
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Showing 4 changed files with 83 additions and 8 deletions.
diff --git a/mimic-iv/buildmimic/sqlite/import.py b/mimic-iv/buildmimic/sqlite/import.py
@@ -50,7 +50,7 @@
 def process_dataframe(df: pd.DataFrame, subjects: t.Optional[t.List[int]] = None) -> pd.DataFrame:
     for c in df.columns:
         if c.endswith('time') or c.endswith('date'):
-            df[c] = pd.to_datetime(df[c])
+            df[c] = pd.to_datetime(df[c], format='ISO8601')
 
     if subjects is not None and 'subject_id' in df:
         df = df.loc[df['subject_id'].isin(subjects)]

diff --git a/mimic-iv/concepts/medication/arb.sql b/mimic-iv/concepts/medication/arb.sql
@@ -2,13 +2,14 @@ WITH arb_drug AS (
   SELECT DISTINCT
     drug
     , CASE
-        WHEN UPPER(drug) LIKE '%AZILSARTAN%' THEN 1
-        WHEN UPPER(drug) LIKE '%CANDESARTAN%' THEN 1
-        WHEN UPPER(drug) LIKE '%IRBESARTAN%' THEN 1
-        WHEN UPPER(drug) LIKE '%LOSARTAN%' THEN 1
-        WHEN UPPER(drug) LIKE '%OLMESARTAN%' THEN 1
-        WHEN UPPER(drug) LIKE '%TELMISARTAN%' THEN 1
-        WHEN UPPER(drug) LIKE '%VALSARTAN%' THEN 1
+        WHEN UPPER(drug) LIKE '%AZILSARTAN%' OR UPPER(drug) LIKE '%EDARBI%' THEN 1
+        WHEN UPPER(drug) LIKE '%CANDESARTAN%' OR UPPER(drug) LIKE '%ATACAND%' THEN 1
+        WHEN UPPER(drug) LIKE '%IRBESARTAN%' OR UPPER(drug) LIKE '%AVAPRO%' THEN 1
+        WHEN UPPER(drug) LIKE '%LOSARTAN%' OR UPPER(drug) LIKE '%COZAAR%' THEN 1
+        WHEN UPPER(drug) LIKE '%OLMESARTAN%' OR UPPER(drug) LIKE '%BENICAR%' THEN 1
+        WHEN UPPER(drug) LIKE '%TELMISARTAN%' OR UPPER(drug) LIKE '%MICARDIS%' THEN 1
+        WHEN UPPER(drug) LIKE '%VALSARTAN%' OR UPPER(drug) LIKE '%DIOVAN%' THEN 1
+        WHEN UPPER(drug) LIKE '%SACUBITRIL%' OR UPPER(drug) LIKE '%ENTRESTO%' THEN 1
         ELSE 0
       END AS arb
   FROM `physionet-data.mimiciv_hosp.prescriptions`

diff --git a/mimic-iv/concepts_duckdb/medication/arb.sql b/mimic-iv/concepts_duckdb/medication/arb.sql
@@ -0,0 +1,37 @@
+-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
+DROP TABLE IF EXISTS mimiciv_derived.arb; CREATE TABLE mimiciv_derived.arb AS
+WITH arb_drug AS (
+  SELECT DISTINCT
+    drug,
+    CASE
+      WHEN UPPER(drug) LIKE '%AZILSARTAN%' OR UPPER(drug) LIKE '%EDARBI%'
+      THEN 1
+      WHEN UPPER(drug) LIKE '%CANDESARTAN%' OR UPPER(drug) LIKE '%ATACAND%'
+      THEN 1
+      WHEN UPPER(drug) LIKE '%IRBESARTAN%' OR UPPER(drug) LIKE '%AVAPRO%'
+      THEN 1
+      WHEN UPPER(drug) LIKE '%LOSARTAN%' OR UPPER(drug) LIKE '%COZAAR%'
+      THEN 1
+      WHEN UPPER(drug) LIKE '%OLMESARTAN%' OR UPPER(drug) LIKE '%BENICAR%'
+      THEN 1
+      WHEN UPPER(drug) LIKE '%TELMISARTAN%' OR UPPER(drug) LIKE '%MICARDIS%'
+      THEN 1
+      WHEN UPPER(drug) LIKE '%VALSARTAN%' OR UPPER(drug) LIKE '%DIOVAN%'
+      THEN 1
+      WHEN UPPER(drug) LIKE '%SACUBITRIL%' OR UPPER(drug) LIKE '%ENTRESTO%'
+      THEN 1
+      ELSE 0
+    END AS arb
+  FROM mimiciv_hosp.prescriptions
+)
+SELECT
+  pr.subject_id,
+  pr.hadm_id,
+  pr.drug AS arb,
+  pr.starttime,
+  pr.stoptime
+FROM mimiciv_hosp.prescriptions AS pr
+INNER JOIN arb_drug
+  ON pr.drug = arb_drug.drug
+WHERE
+  arb_drug.arb = 1
diff --git a/mimic-iv/concepts_postgres/medication/arb.sql b/mimic-iv/concepts_postgres/medication/arb.sql
@@ -0,0 +1,37 @@
+-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
+DROP TABLE IF EXISTS mimiciv_derived.arb; CREATE TABLE mimiciv_derived.arb AS
+WITH arb_drug AS (
+  SELECT DISTINCT
+    drug,
+    CASE
+      WHEN UPPER(drug) LIKE '%AZILSARTAN%' OR UPPER(drug) LIKE '%EDARBI%'
+      THEN 1
+      WHEN UPPER(drug) LIKE '%CANDESARTAN%' OR UPPER(drug) LIKE '%ATACAND%'
+      THEN 1
+      WHEN UPPER(drug) LIKE '%IRBESARTAN%' OR UPPER(drug) LIKE '%AVAPRO%'
+      THEN 1
+      WHEN UPPER(drug) LIKE '%LOSARTAN%' OR UPPER(drug) LIKE '%COZAAR%'
+      THEN 1
+      WHEN UPPER(drug) LIKE '%OLMESARTAN%' OR UPPER(drug) LIKE '%BENICAR%'
+      THEN 1
+      WHEN UPPER(drug) LIKE '%TELMISARTAN%' OR UPPER(drug) LIKE '%MICARDIS%'
+      THEN 1
+      WHEN UPPER(drug) LIKE '%VALSARTAN%' OR UPPER(drug) LIKE '%DIOVAN%'
+      THEN 1
+      WHEN UPPER(drug) LIKE '%SACUBITRIL%' OR UPPER(drug) LIKE '%ENTRESTO%'
+      THEN 1
+      ELSE 0
+    END AS arb
+  FROM mimiciv_hosp.prescriptions
+)
+SELECT
+  pr.subject_id,
+  pr.hadm_id,
+  pr.drug AS arb,
+  pr.starttime,
+  pr.stoptime
+FROM mimiciv_hosp.prescriptions AS pr
+INNER JOIN arb_drug
+  ON pr.drug = arb_drug.drug
+WHERE
+  arb_drug.arb = 1