removed version and author from individual files, better to track in …

…github

Makefile

@@ -1,8 +1,6 @@
 ## ------------------------------------------------------------------
 ## Title: Top-level build file
 ## Description: Automated import of data and SQL scripts
-## MIMIC version: MIMIC-III v1.4
-## Author: Jim Blundell 2016
 ## ------------------------------------------------------------------
 
 ## Parameters ##
@@ -107,4 +105,3 @@ clean:
 	@$(MAKE) -e -C severityscores clean
 
 .PHONY: help mimic mimic-build mimic-download mimic-check mimic-gz mimic-build-gz mimic-check-gz extra etc comorbidity demographics sepsis severityscores
-

buildmimic/apache-drill/drill_create_data.sql

@@ -1,8 +1,6 @@
 -- ------------------------------------------------------------------
 -- Title: Create the MIMIC-III tables
 -- Description: More detailed description explaining the purpose.
--- MIMIC version: MIMIC-III v1.3
--- Created by: paris nicolas
 -- ------------------------------------------------------------------
 
 

buildmimic/docker/Dockerfile

@@ -1,7 +1,5 @@
 FROM postgres:latest
 
-MAINTAINER Aaron J. Masino
-
 # in the docker initialization, we do not build the data
 ENV BUILD_MIMIC 0
 

buildmimic/monetdb/monetdb_create_tables.sql

@@ -1,8 +1,6 @@
 -- ------------------------------------------------------------------
 -- Title: Create the MIMIC-III tables
 -- Description: More detailed description explaining the purpose.
--- MIMIC version: MIMIC-III v1.3
--- Created by: paris nicolas
 -- ------------------------------------------------------------------
 
 CREATE SCHEMA  mimiciii;

buildmimic/monetdb/monetdb_load_data.sql

@@ -1,8 +1,6 @@
 -- ------------------------------------------------------------------
 -- Title: Load data into the MIMIC-III schema
 -- Description: More detailed description explaining the purpose.
--- MIMIC version: MIMIC-III v1.3
--- Created by: paris nicolas
 -- ------------------------------------------------------------------
 
 

comorbidity/postgres/Makefile

@@ -1,8 +1,6 @@
 ## ------------------------------------------------------------------
 ## Title: Build file for comorbidity
 ## Description: Automated import of SQL scripts for comorbidity
-## MIMIC version: MIMIC-III v1.3
-## Author: Jim Blundell 2016
 ## ------------------------------------------------------------------
 
 ## Parameters ##
@@ -38,5 +36,3 @@ clean:
 	@echo '--- Building' $< '---'
 	@echo
 	@$(PSQL) -f $<
-
-

comorbidity/postgres/clean.sql

@@ -1,8 +1,6 @@
--- ------------------------------------------------------------------  
 -- Title: SQL clean script called by "make clean"
 -- Description: Drops all materialized views re: comorbidity scoring
--- MIMIC version: All
--- Author: Jim Blundell 2016
--- ------------------------------------------------------------------  
 
 DROP MATERIALIZED VIEW IF EXISTS ELIXHAUSER_AHRQ CASCADE;

demographics/postgres/Makefile

@@ -1,8 +1,6 @@
 ## ------------------------------------------------------------------
 ## Title: Build file for demographics
 ## Description: Automated import of SQL scripts for demographics
-## MIMIC version: MIMIC-III v1.3
-## Author: Jim Blundell 2016
 ## ------------------------------------------------------------------
 
 ## Parameters ##
@@ -37,5 +35,3 @@ clean:
 	@echo '--- Building' $< '---'
 	@echo
 	@$(PSQL) -f $<
-
-

demographics/postgres/clean.sql

@@ -1,10 +1,7 @@
--- ------------------------------------------------------------------  
 -- Title: SQL clean script called by "make clean"
 -- Description: Drops all materialized views re: demographics
--- MIMIC version: All
--- Author: Jim Blundell 2016
--- ------------------------------------------------------------------  
 
 DROP MATERIALIZED VIEW IF EXISTS icustay_detail CASCADE;
 DROP MATERIALIZED VIEW IF EXISTS heightweight CASCADE;
-

etc/Makefile

@@ -1,8 +1,6 @@
 ## ------------------------------------------------------------------
 ## Title: Build file for etc and etc/firstday
 ## Description: Automated import of SQL scripts for etc and etc/firstday
-## MIMIC version: MIMIC-III v1.3
-## Author: Jim Blundell 2016
 ## ------------------------------------------------------------------
 
 ## Parameters ##
@@ -42,4 +40,3 @@ clean:
 	@echo '--- Building' $< '---'
 	@echo
 	@$(PSQL) -f $<
-

etc/clean.sql

@@ -1,9 +1,7 @@
--- ------------------------------------------------------------------  
 -- Title: SQL clean script called by "make clean"
 -- Description: Drops all materialized views re: misc clinical concepts
--- MIMIC version: All
--- Author: Jim Blundell 2016
--- ------------------------------------------------------------------  
 
 DROP MATERIALIZED VIEW IF EXISTS ECHODATA CASCADE;
 DROP MATERIALIZED VIEW IF EXISTS rrt CASCADE;

etc/firstday/Makefile

@@ -1,9 +1,7 @@
-## ------------------------------------------------------------------  
 ## Title: Build file for etc/firstday
 ## Description: Automated import of SQL scripts for firstday
-## MIMIC version: MIMIC-III v1.3
-## Author: Jim Blundell 2016
-## ------------------------------------------------------------------  
 
 ## Parameters ##
 # The top-level Makefile settings take precedence over this
@@ -35,4 +33,3 @@ clean:
 	@echo '--- Building' $< '---'
 	@echo
 	@$(PSQL) -f $<
-

etc/firstday/blood-gas-first-day.sql

@@ -1,5 +1,3 @@
--- This query is designed for MIMIC-III v1.3
-
 -- The aim of this query is to pivot entries related to blood gases and
 -- chemistry values which were found in LABEVENTS
 

etc/firstday/clean.sql

@@ -1,9 +1,7 @@
--- ------------------------------------------------------------------  
 -- Title: SQL clean script called by "make clean"
 -- Description: Drops all materialized views re: first day concepts
--- MIMIC version: All
--- Author: Jim Blundell 2016
--- ------------------------------------------------------------------  
 
 DROP MATERIALIZED VIEW IF EXISTS bloodgasfirstdayarterial CASCADE;
 DROP MATERIALIZED VIEW IF EXISTS bloodgasfirstday CASCADE;

etc/firstday/urine-output-first-day.sql

@@ -1,8 +1,5 @@
 -- ------------------------------------------------------------------
 -- Purpose: Create a view of the urine output for each ICUSTAY_ID over the first 24 hours.
--- Tested on MIMIC-III v1.2
--- Written by: Alistair E. W. Johnson
--- References: TBA.
 -- ------------------------------------------------------------------
 
 create materialized view uofirstday as

etc/firstday/ventilation-first-day.sql

@@ -1,7 +1,5 @@
 -- Determines if a patient is ventilated on the first day of their ICU stay.
 -- Creates a table with the result.
--- Contact: aewj@mit.edu
--- Copyright 2015, Alistair Johnson
 
 CREATE MATERIALIZED VIEW ventfirstday AS
 -- group together the flags based on icustay_id
@@ -112,7 +110,7 @@ select
   , case
       when ce.itemid = 648 and value = 'Intubated/trach' THEN 1 -- Speech = intubated
     else 0 end as SpeechIntubated
-    
 from icustays ie
 left join chartevents ce
   on ie.icustay_id = ce.icustay_id and ce.value is not null

sepsis/Makefile

@@ -1,8 +1,6 @@
 ## ------------------------------------------------------------------
 ## Title: Build file for sepsis
 ## Description: Automated import of SQL scripts for sepsis
-## MIMIC version: MIMIC-III v1.3
-## Author: Jim Blundell 2016
 ## ------------------------------------------------------------------
 
 ## Parameters ##
@@ -39,5 +37,3 @@ clean:
 	@echo '--- Building' $< '---'
 	@echo
 	@$(PSQL) -f $<
-
-

sepsis/angus.sql

@@ -4,19 +4,17 @@
 -- http://www.ncbi.nlm.nih.gov/pubmed/11445675
 
 -- 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). 
-
--- By Sharukh Lokhandwala and Tom Pollard 2015
 
 -- Appendix 1: ICD9-codes (infection)
 CREATE MATERIALIZED VIEW angus_sepsis as
 
 WITH infection_group AS (
 	SELECT subject_id, hadm_id,
-	CASE 
 		WHEN substring(icd9_code,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',
@@ -36,22 +34,22 @@ WITH infection_group AS (
 -- Appendix 2: ICD9-codes (organ dysfunction)
 	organ_diag_group as (
 	SELECT subject_id, hadm_id,
-		CASE 
 		-- Acute Organ Dysfunction Diagnosis Codes
 		WHEN substring(icd9_code,1,3) IN ('458','293','570','584') THEN 1
 		WHEN substring(icd9_code,1,4) IN ('7855','3483','3481',
-				'2874','2875','2869','2866','5734')  THEN 1	
 		ELSE 0 END AS organ_dysfunction,
 		-- Explicit diagnosis of severe sepsis or septic shock
-		CASE 
 		WHEN substring(icd9_code,1,5) IN ('99592','78552')  THEN 1
 		ELSE 0 END AS explicit_sepsis
 	FROM MIMICIII.DIAGNOSES_ICD),
 
 -- Mechanical ventilation
 	organ_proc_group as (
 	SELECT subject_id, hadm_id,
-		CASE 
 		WHEN substring(icd9_code,1,4) IN ('9670','9671','9672') THEN 1
 		ELSE 0 END AS mech_vent
 	FROM MIMICIII.PROCEDURES_ICD),
@@ -60,11 +58,11 @@ WITH infection_group AS (
 	aggregate as (
 	SELECT subject_id, hadm_id,
 		CASE
-		WHEN hadm_id in (SELECT DISTINCT hadm_id 
 				FROM infection_group
 				WHERE infection = 1) THEN 1
 			ELSE 0 END AS infection,
-		CASE 
 		WHEN hadm_id in (SELECT DISTINCT hadm_id
 				FROM organ_diag_group
 				WHERE explicit_sepsis = 1) THEN 1
@@ -89,4 +87,3 @@ SELECT subject_id, hadm_id, infection,
 	WHEN infection = 1 AND mech_vent = 1 THEN 1
 	ELSE 0 END AS Angus
 FROM aggregate;
-

sepsis/clean.sql

@@ -1,8 +1,6 @@
--- ------------------------------------------------------------------  
 -- Title: SQL clean script called by "make clean"
 -- Description: Drops all materialized views re: sepsis
--- MIMIC version: All
--- Author: Jim Blundell 2016
--- ------------------------------------------------------------------  
 
 DROP MATERIALIZED VIEW IF EXISTS angus_sepsis CASCADE;

severityscores/Makefile

@@ -1,8 +1,6 @@
 ## ------------------------------------------------------------------
 ## Title: Build file for severityscores
 ## Description: Automated import of SQL scripts for severityscores
-## MIMIC version: MIMIC-III v1.3
-## Author: Jim Blundell 2016
 ## ------------------------------------------------------------------
 
 ## Parameters ##
@@ -38,4 +36,3 @@ clean:
 	@echo '--- Building' $< '---'
 	@echo
 	@$(PSQL) -f $<
-

severityscores/apsiii.sql

@@ -1,15 +1,9 @@
 -- ------------------------------------------------------------------
 -- Title: Acute Physiology Score III (APS III)
--- MIMIC version: MIMIC-III v1.4
--- Originally written by: Alistair Johnson
--- Contact: aewj [at] mit [dot] edu
--- ------------------------------------------------------------------
-
 -- This query extracts the acute physiology score III.
 -- This score is a measure of patient severity of illness.
 -- The score is calculated on the first day of each ICU patients' stay.
--- The score is calculated for *all* ICU patients, with the assumption that the user will subselect appropriate ICUSTAY_IDs.
--- For example, the score is calculated for neonates, but it is likely inappropriate to actually use the score values for these patients.
 
 -- Reference for APS III:
 --    Knaus WA, Wagner DP, Draper EA, Zimmerman JE, Bergner M, Bastos PG, Sirio CA, Murphy DJ, Lotring T, Damiano A.
@@ -35,6 +29,9 @@
 --  4) gcsfirstday - generated by gcs-first-day.sql
 --  5) labsfirstday - generated by labs-first-day.sql
 
+-- Note:
+--  The score is calculated for *all* ICU patients, with the assumption that the user will subselect appropriate ICUSTAY_IDs.
+--  For example, the score is calculated for neonates, but it is likely inappropriate to actually use the score values for these patients.
 
 -- List of TODO:
 -- The site of temperature is not incorporated. Axillary measurements should be increased by 1 degree.

severityscores/clean.sql

@@ -1,9 +1,7 @@
--- ------------------------------------------------------------------  
 -- Title: SQL clean script called by "make clean"
 -- Description: Drops all materialized views re: severity scores
--- MIMIC version: All
--- Author: Jim Blundell 2016
--- ------------------------------------------------------------------  
 
 DROP MATERIALIZED VIEW IF EXISTS APSIII CASCADE;
 DROP MATERIALIZED VIEW IF EXISTS LODS CASCADE;

severityscores/lods.sql

@@ -1,17 +1,9 @@
 -- ------------------------------------------------------------------
 -- Title: Logistic Organ Dysfunction Score (LODS)
--- MIMIC version: MIMIC-III v1.4
--- Originally written as sofa.sql by: Alistair Johnson
--- Edited as lods.sql by: Josh Gieringer
--- Contact: aewj [at] mit [dot] edu
--- Contact: joshua [dot] gieringer [at] digitalreasoning [dot] com
--- ------------------------------------------------------------------
-
 -- This query extracts the logistic organ dysfunction system.
 -- This score is a measure of organ failure in a patient.
 -- The score is calculated on the first day of each ICU patients' stay.
--- The score is calculated for *all* ICU patients, with the assumption that the user will subselect appropriate ICUSTAY_IDs.
--- For example, the score is calculated for neonates, but it is likely inappropriate to actually use the score values for these patients.
 
 -- Reference for LODS:
 --  Le Gall, J. R., Klar, J., Lemeshow, S., Saulnier, F., Alberti, C., Artigas, A., & Teres, D.
@@ -34,6 +26,10 @@
 --  5) labsfirstday - generated by labs-first-day.sql
 --  5) bloodgasfirstdayarterial - generated by blood-gas-first-day-arterial.sql
 
+-- Note:
+--  The score is calculated for *all* ICU patients, with the assumption that the user will subselect appropriate ICUSTAY_IDs.
+--  For example, the score is calculated for neonates, but it is likely inappropriate to actually use the score values for these patients.
+
 CREATE MATERIALIZED VIEW LODS as
 -- extract CPAP from the "Oxygen Delivery Device" fields
 with cpap as

severityscores/mlods.sql

@@ -1,12 +1,9 @@
 -- ------------------------------------------------------------------
 -- Title: Modified Logistic organ dysfunction system (mLODS)
--- Originally written by: Alistair Johnson
--- Contact: aewj [at] mit [dot] edu
--- ------------------------------------------------------------------
-
 -- This query extracts a modified version of the logistic organ dysfunction system.
 -- This score was used in the third international definition of sepsis: Sepsis-3.
 -- This score is a measure of organ failure in a patient.
+-- ------------------------------------------------------------------
 
 -- Reference for LODS:
 --  Le Gall, J. R., Klar, J., Lemeshow, S., Saulnier, F., Alberti, C., Artigas, A., & Teres, D.
@@ -28,6 +25,10 @@
 -- Variables *excluded*, that are used in the original LODS:
 --  prothrombin time (PT), blood urea nitrogen, urine output
 
+-- Note:
+--  The score is calculated for *all* ICU patients, with the assumption that the user will subselect appropriate ICUSTAY_IDs.
+--  For example, the score is calculated for neonates, but it is likely inappropriate to actually use the score values for these patients.
+
 CREATE MATERIALIZED VIEW MLODS as
 -- extract CPAP from the "Oxygen Delivery Device" fields
 with cpap as