Materialized view of Angus sepsis

concepts/angus_sepsis.sql

@@ -0,0 +1,110 @@
+-- ------------------------------------------------------------------
+-- Title: Query to create materialized view of Angus sepsis criteria
+-- Description: This code is based on the angus_sepsis query for MIMIC 
+-- https://github.com/MIT-LCP/mimic-code/blob/master/concepts/sepsis/angus.sql
+-- 
+-- Case selection and definitions
+-- To identify cases with severe sepsis, we selected all acute care
+-- hospitalizations with ICD-9-CM codes for both:
+-- (a) a bacterial or fungal infectious process AND
+-- (b) a diagnosis of acute organ dysfunction (Appendix 2).
+-- eICU version: v1.1 
+-- References: Angus et al, 2001. Epidemiology of severe sepsis in 
+-- the United States http://www.ncbi.nlm.nih.gov/pubmed/11445675. 
+-- ------------------------------------------------------------------
+
+SET search_path TO eicu;
+
+DROP MATERIALIZED VIEW IF EXISTS angus_sepsis CASCADE;
+CREATE MATERIALIZED VIEW angus_sepsis as
+
+-- ICD-9 codes for infection - as sourced from Appendix 1 of above paper
+WITH infection_group AS
+(
+    SELECT patientUnitStayID, 
+    CASE
+    	WHEN substring(icd9code,1,3) IN ('001','002','003','004','005','008',
+			   '009','010','011','012','013','014','015','016','017','018',
+			   '020','021','022','023','024','025','026','027','030','031',
+			   '032','033','034','035','036','037','038','039','040','041',
+			   '090','091','092','093','094','095','096','097','098','100',
+			   '101','102','103','104','110','111','112','114','115','116',
+			   '117','118','320','322','324','325','420','421','451','461',
+			   '462','463','464','465','481','482','485','486','494','510',
+			   '513','540','541','542','566','567','590','597','601','614',
+			   '615','616','681','682','683','686','730') THEN 1
+		WHEN substring(icd9code,1,5) IN ('569.5','572.0','572.1','575.0','599.0','711.0',
+				'790.7','996.6','998.5','999.3') THEN 1
+		WHEN substring(icd9code,1,6) IN ('491.21','562.01','562.03','562.11','562.13',
+				'569.83') THEN 1
+		ELSE 0 END AS infection 
+        FROM diagnosis
+),
+-- ICD-9 codes for organ dysfunction - as sourced from Appendix 2 of above paper
+organ_diag_group AS
+(
+    SELECT patientUnitStayID,
+    CASE
+    	WHEN substring(icd9code,1,3) IN ('458','293','570','584') THEN 1
+		WHEN substring(icd9code,1,5) IN ('785.5','348.3','348.1',
+				'287.4','287.5','286.9','286.6','573.4')  THEN 1
+		ELSE 0 END AS organ_dysfunction,
+		-- Explicit diagnosis of severe sepsis or septic shock
+		CASE
+		WHEN substring(icd9code,1,6) IN ('995.92','785.52')  THEN 1
+		ELSE 0 END AS explicit_sepsis
+	FROM diagnosis
+),
+-- Mechanical ventilation
+organ_proc_group as
+(
+	SELECT patientUnitStayID,
+		CASE
+		WHEN treatmentstring LIKE '%mechanical ventilation%' THEN 1
+		ELSE 0 END AS mech_vent
+	FROM treatment
+),
+-- Aggregate above views together
+aggregate as
+(
+	SELECT patientUnitStayID,
+		CASE
+			WHEN patientUnitStayID in
+					(SELECT DISTINCT patientUnitStayID
+					FROM infection_group
+					WHERE infection = 1)
+				THEN 1
+			ELSE 0 END AS infection,
+		CASE
+			WHEN patientUnitStayID in
+					(SELECT DISTINCT patientUnitStayID
+					FROM organ_diag_group
+					WHERE explicit_sepsis = 1)
+				THEN 1
+			ELSE 0 END AS explicit_sepsis,
+		CASE
+			WHEN patientUnitStayID in
+					(SELECT DISTINCT patientUnitStayID
+					FROM organ_diag_group
+					WHERE organ_dysfunction = 1)
+				THEN 1
+			ELSE 0 END AS organ_dysfunction,
+		CASE
+		WHEN patientUnitStayID in
+				(SELECT DISTINCT patientUnitStayID
+				FROM organ_proc_group
+				WHERE mech_vent = 1)
+			THEN 1
+		ELSE 0 END AS mech_vent
+	FROM patient
+)
+-- Output component flags (explicit sepsis, organ dysfunction) and final flag (angus)
+SELECT patientUnitStayID, infection,
+   explicit_sepsis, organ_dysfunction, mech_vent,
+CASE
+	WHEN explicit_sepsis = 1 THEN 1
+	WHEN infection = 1 AND organ_dysfunction = 1 THEN 1
+	WHEN infection = 1 AND mech_vent = 1 THEN 1
+	ELSE 0 END
+AS angus
+FROM aggregate;