diff --git a/buildmimic/monetdb/monetdb_load_data.sql b/buildmimic/monetdb/monetdb_load_data.sql index 831698a..1f2ca95 100644 --- a/buildmimic/monetdb/monetdb_load_data.sql +++ b/buildmimic/monetdb/monetdb_load_data.sql @@ -1,9 +1,9 @@ --- ------------------------------------------------------------------ --- 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 --- ------------------------------------------------------------------ +-- ------------------------------------------------------------------ +-- 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 +-- ------------------------------------------------------------------ /* Set the mimic_data_dir variable to point to directory containing @@ -35,7 +35,7 @@ COPY 7567 OFFSET 2 RECORDS INTO MIMICIII.CAREGIVERS FROM '/path/to/CAREGIVERS.cs -- Load Data for Table CHARTEVENTS -------------------------------------------------------- -COPY 263201375 OFFSET 2 RECORDS INTO MIMICIII.CHARTEVENTS FROM '/path/to/CHARTEVENTS.csv' USING DELIMITERS ',','\n','"' NULL AS ''; +COPY 330712483 OFFSET 2 RECORDS INTO MIMICIII.CHARTEVENTS FROM '/path/to/CHARTEVENTS.csv' USING DELIMITERS ',','\n','"' NULL AS ''; ---------------------------------------------------------------------------------------------------------------- -- Load Data for Table CPTEVENTS @@ -47,13 +47,13 @@ COPY 573146 OFFSET 2 RECORDS INTO MIMICIII.CPTEVENTS FROM '/path/to/CPTEVENTS.cs -- Load Data for Table DATETIMEEVENTS -------------------------------------------------------- -COPY 4486049 OFFSET 2 RECORDS INTO MIMICIII.DATETIMEEVENTS FROM '/path/to/DATETIMEEVENTS.csv' USING DELIMITERS ',','\n','"' NULL AS ''; +COPY 4485937 OFFSET 2 RECORDS INTO MIMICIII.DATETIMEEVENTS FROM '/path/to/DATETIMEEVENTS.csv' USING DELIMITERS ',','\n','"' NULL AS ''; -------------------------------------------------------- -- Load Data for Table DIAGNOSES_ICD -------------------------------------------------------- -COPY 651048 OFFSET 2 RECORDS INTO MIMICIII.DIAGNOSES_ICD FROM '/path/to/DIAGNOSES_ICD.csv' USING DELIMITERS ',','\n','"' NULL AS ''; +COPY 651047 OFFSET 2 RECORDS INTO MIMICIII.DIAGNOSES_ICD FROM '/path/to/DIAGNOSES_ICD.csv' USING DELIMITERS ',','\n','"' NULL AS ''; -------------------------------------------------------- -- Load Data for Table DRGCODES @@ -89,7 +89,7 @@ COPY 12478 OFFSET 2 RECORDS INTO MIMICIII.D_ITEMS FROM '/path/to/D_ITEMS.csv' US -- Load Data for Table D_LABITEMS -------------------------------------------------------- -COPY 755 OFFSET 2 RECORDS INTO MIMICIII.D_LABITEMS FROM '/path/to/D_LABITEMS.csv' USING DELIMITERS ',','\n','"' NULL AS ''; +COPY 753 OFFSET 2 RECORDS INTO MIMICIII.D_LABITEMS FROM '/path/to/D_LABITEMS.csv' USING DELIMITERS ',','\n','"' NULL AS ''; -------------------------------------------------------- -- Load Data for Table ICUSTAYS @@ -101,7 +101,7 @@ COPY 61532 OFFSET 2 RECORDS INTO MIMICIII.ICUSTAYS FROM '/path/to/ICUSTAYS.csv' -- Load Data for Table INPUTEVENTS_CV -------------------------------------------------------- -COPY 17528894 OFFSET 2 RECORDS INTO MIMICIII.INPUTEVENTS_CV FROM '/path/to/INPUTEVENTS_CV.csv' USING DELIMITERS ',','\n','"' NULL AS ''; +COPY 17527935 OFFSET 2 RECORDS INTO MIMICIII.INPUTEVENTS_CV FROM '/path/to/INPUTEVENTS_CV.csv' USING DELIMITERS ',','\n','"' NULL AS ''; -------------------------------------------------------- -- Load Data for Table INPUTEVENTS_MV @@ -113,25 +113,25 @@ COPY 3618991 OFFSET 2 RECORDS INTO MIMICIII.INPUTEVENTS_MV FROM '/path/to/INPUTE -- Load Data for Table LABEVENTS -------------------------------------------------------- -COPY 27872575 OFFSET 2 RECORDS INTO MIMICIII.LABEVENTS FROM '/path/to/LABEVENTS.csv' USING DELIMITERS ',','\n','"' NULL AS ''; +COPY 27854055 OFFSET 2 RECORDS INTO MIMICIII.LABEVENTS FROM '/path/to/LABEVENTS.csv' USING DELIMITERS ',','\n','"' NULL AS ''; -------------------------------------------------------- -- Load Data for Table MICROBIOLOGYEVENTS -------------------------------------------------------- -COPY 328446 OFFSET 2 RECORDS INTO MIMICIII.MICROBIOLOGYEVENTS FROM '/path/to/MICROBIOLOGYEVENTS.csv' USING DELIMITERS ',','\n','"' NULL AS ''; +COPY 631726 OFFSET 2 RECORDS INTO MIMICIII.MICROBIOLOGYEVENTS FROM '/path/to/MICROBIOLOGYEVENTS.csv' USING DELIMITERS ',','\n','"' NULL AS ''; -------------------------------------------------------- -- Load Data for Table NOTEEVENTS -------------------------------------------------------- -COPY 2078704 OFFSET 2 RECORDS INTO MIMICIII.NOTEEVENTS FROM '/path/to/NOTEEVENTS.csv' USING DELIMITERS ',','\n','"' NULL AS ''; +COPY 2083180 OFFSET 2 RECORDS INTO MIMICIII.NOTEEVENTS FROM '/path/to/NOTEEVENTS.csv' USING DELIMITERS ',','\n','"' NULL AS ''; -------------------------------------------------------- -- Load Data for Table OUTPUTEVENTS -------------------------------------------------------- -COPY 349339 OFFSET 2 RECORDS INTO MIMICIII.OUTPUTEVENTS FROM '/path/to/OUTPUTEVENTS.csv' USING DELIMITERS ',','\n','"' NULL AS ''; +COPY 4349218 OFFSET 2 RECORDS INTO MIMICIII.OUTPUTEVENTS FROM '/path/to/OUTPUTEVENTS.csv' USING DELIMITERS ',','\n','"' NULL AS ''; -------------------------------------------------------- -- Load Data for Table PATIENTS @@ -143,7 +143,7 @@ COPY 46520 OFFSET 2 RECORDS INTO MIMICIII.PATIENTS FROM '/path/to/PATIENTS.csv' -- Load Data for Table PRESCRIPTIONS -------------------------------------------------------- -COPY 156848 OFFSET 2 RECORDS INTO MIMICIII.PRESCRIPTIONS FROM '/path/to/PRESCRIPTIONS.csv' USING DELIMITERS ',','\n','"' NULL AS ''; +COPY 4156450 OFFSET 2 RECORDS INTO MIMICIII.PRESCRIPTIONS FROM '/path/to/PRESCRIPTIONS.csv' USING DELIMITERS ',','\n','"' NULL AS ''; -------------------------------------------------------- -- Load Data for Table PROCEDUREEVENTS_MV diff --git a/etc/firstday/lab-first-day.sql b/etc/firstday/labs-first-day.sql similarity index 94% rename from etc/firstday/lab-first-day.sql rename to etc/firstday/labs-first-day.sql index 9141791..66daba8 100644 --- a/etc/firstday/lab-first-day.sql +++ b/etc/firstday/labs-first-day.sql @@ -2,7 +2,7 @@ -- Have already confirmed that the unit of measurement is always the same: null or the correct unit -drop materialized view IF EXISTS labsfirstday; +drop materialized view IF EXISTS labsfirstday CASCADE; create materialized view labsfirstday as select @@ -12,6 +12,8 @@ select , max(case when label = 'ANION GAP' then valuenum else null end) as ANIONGAP_max , min(case when label = 'ALBUMIN' then valuenum else null end) as ALBUMIN_min , max(case when label = 'ALBUMIN' then valuenum else null end) as ALBUMIN_max + , min(case when label = 'BANDS' then valuenum else null end) as BANDS_min + , max(case when label = 'BANDS' then valuenum else null end) as BANDS_max , min(case when label = 'BICARBONATE' then valuenum else null end) as BICARBONATE_min , max(case when label = 'BICARBONATE' then valuenum else null end) as BICARBONATE_max , min(case when label = 'BILIRUBIN' then valuenum else null end) as BILIRUBIN_min @@ -54,6 +56,7 @@ from , case when itemid = 50868 then 'ANION GAP' when itemid = 50862 then 'ALBUMIN' + when itemid = 51144 then 'BANDS' when itemid = 50882 then 'BICARBONATE' when itemid = 50885 then 'BILIRUBIN' when itemid = 50912 then 'CREATININE' @@ -84,6 +87,8 @@ from case when itemid = 50862 and valuenum > 10 then null -- g/dL 'ALBUMIN' when itemid = 50868 and valuenum > 10000 then null -- mEq/L 'ANION GAP' + when itemid = 51144 and valuenum < 0 then null -- immature band forms, % + when itemid = 51144 and valuenum > 100 then null -- immature band forms, % when itemid = 50882 and valuenum > 10000 then null -- mEq/L 'BICARBONATE' when itemid = 50885 and valuenum > 150 then null -- mg/dL 'BILIRUBIN' when itemid = 50806 and valuenum > 10000 then null -- mEq/L 'CHLORIDE' @@ -120,6 +125,7 @@ from -- comment is: LABEL | CATEGORY | FLUID | NUMBER OF ROWS IN LABEVENTS 50868, -- ANION GAP | CHEMISTRY | BLOOD | 769895 50862, -- ALBUMIN | CHEMISTRY | BLOOD | 146697 + 51144, -- BANDS - hematology 50882, -- BICARBONATE | CHEMISTRY | BLOOD | 780733 50885, -- BILIRUBIN, TOTAL | CHEMISTRY | BLOOD | 238277 50912, -- CREATININE | CHEMISTRY | BLOOD | 797476