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Add missing Postgres concepts for Sepsis-3 and SOFA pivot logic (MIMIC-III) #1963

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196 changes: 196 additions & 0 deletions mimic-iii/concepts_postgres/pivot/pivoted_bg.sql
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-- =====================================================================
-- PostgreSQL version of BigQuery pivoted-bg.sql (MIMIC-III)
-- Purpose: Pivot blood gas / chemistry values from labevents, and assign
-- them to an icustay_id using fuzzy ICU boundaries.
--
-- Expected schemas (recommended for PR):
-- mimiciii_clinical: raw MIMIC-III tables (icustays, labevents, admissions)
-- mimiciii_derived : derived concepts output schema (where this table lives)
--
-- Dependencies:
-- - postgres-functions.sql should be loaded (for DATETIME_ADD/SUB/DIFF)
-- NOTE: This script only uses DATETIME_ADD/SUB/DIFF style patterns,
-- but is also valid if you replace them with native +/- intervals.
--
-- Output table name (suggested):
-- mimiciii_derived.pivoted_bg
-- =====================================================================

DROP TABLE IF EXISTS mimiciii_derived.pivoted_bg;

CREATE TABLE mimiciii_derived.pivoted_bg AS
WITH i AS
(
SELECT
subject_id
, icustay_id
, intime
, outtime
, LAG(outtime) OVER (PARTITION BY subject_id ORDER BY intime) AS outtime_lag
, LEAD(intime) OVER (PARTITION BY subject_id ORDER BY intime) AS intime_lead
FROM mimiciii_clinical.icustays
)
, iid_assign AS
(
SELECT
i.subject_id
, i.icustay_id
, CASE
WHEN i.outtime_lag IS NOT NULL
AND i.outtime_lag > (i.intime - INTERVAL '24' HOUR)
THEN i.intime
- (INTERVAL '1' HOUR
* CAST(ROUND( (EXTRACT(EPOCH FROM (i.intime - i.outtime_lag)) / 3600.0) / 2.0 ) AS BIGINT))
ELSE i.intime - INTERVAL '12' HOUR
END AS data_start
, CASE
WHEN i.intime_lead IS NOT NULL
AND i.intime_lead < (i.outtime + INTERVAL '24' HOUR)
THEN i.outtime
+ (INTERVAL '1' MINUTE
* CAST(ROUND( (EXTRACT(EPOCH FROM (i.intime_lead - i.outtime)) / 60.0) / 2.0 ) AS BIGINT))
ELSE i.outtime + INTERVAL '12' HOUR
END AS data_end
FROM i
)
, pvt AS
(
SELECT
le.hadm_id
, CASE
WHEN le.itemid = 50800 THEN 'SPECIMEN'
WHEN le.itemid = 50801 THEN 'AADO2'
WHEN le.itemid = 50802 THEN 'BASEEXCESS'
WHEN le.itemid = 50803 THEN 'BICARBONATE'
WHEN le.itemid = 50804 THEN 'TOTALCO2'
WHEN le.itemid = 50805 THEN 'CARBOXYHEMOGLOBIN'
WHEN le.itemid = 50806 THEN 'CHLORIDE'
WHEN le.itemid = 50808 THEN 'CALCIUM'
WHEN le.itemid = 50809 THEN 'GLUCOSE'
WHEN le.itemid = 50810 THEN 'HEMATOCRIT'
WHEN le.itemid = 50811 THEN 'HEMOGLOBIN'
WHEN le.itemid = 50812 THEN 'INTUBATED'
WHEN le.itemid = 50813 THEN 'LACTATE'
WHEN le.itemid = 50814 THEN 'METHEMOGLOBIN'
WHEN le.itemid = 50815 THEN 'O2FLOW'
WHEN le.itemid = 50816 THEN 'FIO2'
WHEN le.itemid = 50817 THEN 'SO2'
WHEN le.itemid = 50818 THEN 'PCO2'
WHEN le.itemid = 50819 THEN 'PEEP'
WHEN le.itemid = 50820 THEN 'PH'
WHEN le.itemid = 50821 THEN 'PO2'
WHEN le.itemid = 50822 THEN 'POTASSIUM'
WHEN le.itemid = 50823 THEN 'REQUIREDO2'
WHEN le.itemid = 50824 THEN 'SODIUM'
WHEN le.itemid = 50825 THEN 'TEMPERATURE'
WHEN le.itemid = 50826 THEN 'TIDALVOLUME'
WHEN le.itemid = 50827 THEN 'VENTILATIONRATE'
WHEN le.itemid = 50828 THEN 'VENTILATOR'
ELSE NULL
END AS label
, le.charttime
, le.value
, CASE
WHEN le.valuenum IS NULL THEN NULL
WHEN le.valuenum <= 0 THEN NULL
WHEN le.itemid = 50810 AND le.valuenum > 100 THEN NULL -- hematocrit
WHEN le.itemid = 50816 AND le.valuenum < 20 THEN NULL -- fio2 lower bound
WHEN le.itemid = 50816 AND le.valuenum > 100 THEN NULL -- fio2 upper bound
WHEN le.itemid = 50817 AND le.valuenum > 100 THEN NULL -- o2 sat
WHEN le.itemid = 50815 AND le.valuenum > 70 THEN NULL -- o2 flow
WHEN le.itemid = 50821 AND le.valuenum > 800 THEN NULL -- po2
ELSE le.valuenum
END AS valuenum
FROM mimiciii_clinical.labevents le
WHERE le.itemid IN
(
50800, 50801, 50802, 50803, 50804, 50805, 50806, 50807, 50808, 50809
, 50810, 50811, 50812, 50813, 50814, 50815, 50816, 50817, 50818, 50819
, 50820, 50821, 50822, 50823, 50824, 50825, 50826, 50827, 50828
, 51545
)
)
, grp AS
(
SELECT
pvt.hadm_id
, pvt.charttime
, MAX(CASE WHEN label = 'SPECIMEN' THEN value ELSE NULL END) AS specimen
, AVG(CASE WHEN label = 'AADO2' THEN valuenum ELSE NULL END) AS aado2
, AVG(CASE WHEN label = 'BASEEXCESS' THEN valuenum ELSE NULL END) AS baseexcess
, AVG(CASE WHEN label = 'BICARBONATE' THEN valuenum ELSE NULL END) AS bicarbonate
, AVG(CASE WHEN label = 'TOTALCO2' THEN valuenum ELSE NULL END) AS totalco2
, AVG(CASE WHEN label = 'CARBOXYHEMOGLOBIN' THEN valuenum ELSE NULL END) AS carboxyhemoglobin
, AVG(CASE WHEN label = 'CHLORIDE' THEN valuenum ELSE NULL END) AS chloride
, AVG(CASE WHEN label = 'CALCIUM' THEN valuenum ELSE NULL END) AS calcium
, AVG(CASE WHEN label = 'GLUCOSE' THEN valuenum ELSE NULL END) AS glucose
, AVG(CASE WHEN label = 'HEMATOCRIT' THEN valuenum ELSE NULL END) AS hematocrit
, AVG(CASE WHEN label = 'HEMOGLOBIN' THEN valuenum ELSE NULL END) AS hemoglobin
, AVG(CASE WHEN label = 'INTUBATED' THEN valuenum ELSE NULL END) AS intubated
, AVG(CASE WHEN label = 'LACTATE' THEN valuenum ELSE NULL END) AS lactate
, AVG(CASE WHEN label = 'METHEMOGLOBIN' THEN valuenum ELSE NULL END) AS methemoglobin
, AVG(CASE WHEN label = 'O2FLOW' THEN valuenum ELSE NULL END) AS o2flow
, AVG(CASE WHEN label = 'FIO2' THEN valuenum ELSE NULL END) AS fio2
, AVG(CASE WHEN label = 'SO2' THEN valuenum ELSE NULL END) AS so2
, AVG(CASE WHEN label = 'PCO2' THEN valuenum ELSE NULL END) AS pco2
, AVG(CASE WHEN label = 'PEEP' THEN valuenum ELSE NULL END) AS peep
, AVG(CASE WHEN label = 'PH' THEN valuenum ELSE NULL END) AS ph
, AVG(CASE WHEN label = 'PO2' THEN valuenum ELSE NULL END) AS po2
, AVG(CASE WHEN label = 'POTASSIUM' THEN valuenum ELSE NULL END) AS potassium
, AVG(CASE WHEN label = 'REQUIREDO2' THEN valuenum ELSE NULL END) AS requiredo2
, AVG(CASE WHEN label = 'SODIUM' THEN valuenum ELSE NULL END) AS sodium
, AVG(CASE WHEN label = 'TEMPERATURE' THEN valuenum ELSE NULL END) AS temperature
, AVG(CASE WHEN label = 'TIDALVOLUME' THEN valuenum ELSE NULL END) AS tidalvolume
, MAX(CASE WHEN label = 'VENTILATIONRATE' THEN valuenum ELSE NULL END) AS ventilationrate
, MAX(CASE WHEN label = 'VENTILATOR' THEN valuenum ELSE NULL END) AS ventilator
, SUM(CASE WHEN label = 'SPECIMEN' THEN 1 ELSE 0 END) AS specimen_ct
FROM pvt
GROUP BY pvt.hadm_id, pvt.charttime
HAVING SUM(CASE WHEN label = 'SPECIMEN' THEN 1 ELSE 0 END) < 2
)
SELECT
iid.icustay_id
, grp.hadm_id
, grp.charttime
, grp.specimen
, grp.aado2
, grp.baseexcess
, grp.bicarbonate
, grp.totalco2
, grp.carboxyhemoglobin
, grp.chloride
, grp.calcium
, grp.glucose
, grp.hematocrit
, grp.hemoglobin
, grp.intubated
, grp.lactate
, grp.methemoglobin
, grp.o2flow
, grp.fio2
, grp.so2
, grp.pco2
, grp.peep
, grp.ph
, grp.po2
, grp.potassium
, grp.requiredo2
, grp.sodium
, grp.temperature
, grp.tidalvolume
, grp.ventilationrate
, grp.ventilator
FROM grp
INNER JOIN mimiciii_clinical.admissions adm
ON grp.hadm_id = adm.hadm_id
LEFT JOIN iid_assign iid
ON adm.subject_id = iid.subject_id
AND grp.charttime >= iid.data_start
AND grp.charttime < iid.data_end
ORDER BY grp.hadm_id, grp.charttime;

-- Suggested indexes (optional, but helps downstream joins a lot):
-- CREATE INDEX IF NOT EXISTS idx_pivoted_bg_icustay_charttime
-- ON mimiciii_derived.pivoted_bg (icustay_id, charttime);
-- CREATE INDEX IF NOT EXISTS idx_pivoted_bg_hadm_charttime
-- ON mimiciii_derived.pivoted_bg (hadm_id, charttime);
174 changes: 174 additions & 0 deletions mimic-iii/concepts_postgres/pivot/pivoted_bg_art.sql
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-- =====================================================================
-- PostgreSQL version of BigQuery pivoted-bg-art.sql (MIMIC-III)
-- Requires: mimiciii_derived.pivoted_bg
--
-- Output: mimiciii_derived.pivoted_bg_art
-- =====================================================================

DROP TABLE IF EXISTS mimiciii_derived.pivoted_bg_art;

CREATE TABLE mimiciii_derived.pivoted_bg_art AS
WITH stg_spo2 AS
(
SELECT
hadm_id
, charttime
, AVG(valuenum) AS spo2
FROM mimiciii_clinical.chartevents
WHERE itemid IN (646, 220277) -- SpO2
AND valuenum > 0 AND valuenum <= 100
AND charttime IS NOT NULL
GROUP BY hadm_id, charttime
)
, stg_fio2 AS
(
SELECT
hadm_id
, charttime
, MAX(
CASE
WHEN itemid = 223835 THEN
CASE
WHEN valuenum > 0 AND valuenum <= 1 THEN valuenum * 100
WHEN valuenum > 1 AND valuenum < 21 THEN NULL
WHEN valuenum >= 21 AND valuenum <= 100 THEN valuenum
ELSE NULL
END
WHEN itemid IN (3420, 3422) THEN
valuenum
WHEN itemid = 190 AND valuenum > 0.20 AND valuenum < 1 THEN
valuenum * 100
ELSE NULL
END
) AS fio2_chartevents
FROM mimiciii_clinical.chartevents
WHERE itemid IN (3420, 190, 223835, 3422)
AND valuenum > 0 AND valuenum < 100
AND charttime IS NOT NULL
-- exclude rows marked as error (if column exists in your import)
AND (error IS NULL OR error <> 1)
GROUP BY hadm_id, charttime
)
, stg2 AS
(
SELECT
bg.*
, ROW_NUMBER() OVER
(PARTITION BY bg.hadm_id, bg.charttime
ORDER BY s1.charttime DESC NULLS LAST) AS lastrowspo2
, s1.spo2
FROM mimiciii_derived.pivoted_bg bg
LEFT JOIN stg_spo2 s1
ON bg.hadm_id = s1.hadm_id
AND s1.charttime BETWEEN (bg.charttime - INTERVAL '2' HOUR) AND bg.charttime
WHERE bg.po2 IS NOT NULL
)
, stg3 AS
(
SELECT
bg.*
, ROW_NUMBER() OVER
(PARTITION BY bg.hadm_id, bg.charttime
ORDER BY s2.charttime DESC NULLS LAST) AS lastrowfio2
, s2.fio2_chartevents

-- Logistic regression probability (same coefficients as BigQuery)
, 1.0 / (1.0 + EXP(-(
-0.02544
+ 0.04598 * po2
+ COALESCE(-0.15356 * spo2 , -0.15356 * 97.49420 + 0.13429)
+ COALESCE( 0.00621 * fio2_chartevents, 0.00621 * 51.49550 - 0.24958)
+ COALESCE( 0.10559 * hemoglobin , 0.10559 * 10.32307 + 0.05954)
+ COALESCE( 0.13251 * so2 , 0.13251 * 93.66539 - 0.23172)
+ COALESCE(-0.01511 * pco2 , -0.01511 * 42.08866 - 0.01630)
+ COALESCE( 0.01480 * fio2 , 0.01480 * 63.97836 - 0.31142)
+ COALESCE(-0.00200 * aado2 , -0.00200 * 442.21186 - 0.01328)
+ COALESCE(-0.03220 * bicarbonate , -0.03220 * 22.96894 - 0.06535)
+ COALESCE( 0.05384 * totalco2 , 0.05384 * 24.72632 - 0.01405)
+ COALESCE( 0.08202 * lactate , 0.08202 * 3.06436 + 0.06038)
+ COALESCE( 0.10956 * ph , 0.10956 * 7.36233 - 0.00617)
+ COALESCE( 0.00848 * o2flow , 0.00848 * 7.59362 - 0.35803)
))) AS specimen_prob
FROM stg2 bg
LEFT JOIN stg_fio2 s2
ON bg.hadm_id = s2.hadm_id
AND s2.charttime BETWEEN (bg.charttime - INTERVAL '4' HOUR) AND bg.charttime
AND s2.fio2_chartevents > 0
WHERE bg.lastrowspo2 = 1
)
SELECT
stg3.hadm_id
, stg3.icustay_id
, stg3.charttime
, stg3.specimen

, CASE
WHEN stg3.specimen IS NOT NULL THEN stg3.specimen
WHEN stg3.specimen_prob > 0.75 THEN 'ART'
ELSE NULL
END AS specimen_pred
, stg3.specimen_prob

-- oxygen related parameters
, stg3.so2
, stg3.spo2
, stg3.po2
, stg3.pco2
, stg3.fio2_chartevents
, stg3.fio2
, stg3.aado2

, CASE
WHEN stg3.po2 IS NOT NULL
AND stg3.pco2 IS NOT NULL
AND COALESCE(stg3.fio2, stg3.fio2_chartevents) IS NOT NULL
THEN (COALESCE(stg3.fio2, stg3.fio2_chartevents) / 100.0) * (760 - 47) - (stg3.pco2 / 0.8) - stg3.po2
ELSE NULL
END AS aado2_calc

, CASE
WHEN stg3.po2 IS NOT NULL
AND COALESCE(stg3.fio2, stg3.fio2_chartevents) IS NOT NULL
THEN 100.0 * stg3.po2 / COALESCE(stg3.fio2, stg3.fio2_chartevents)
ELSE NULL
END AS pao2fio2ratio

-- acid-base parameters
, stg3.ph
, stg3.baseexcess
, stg3.bicarbonate
, stg3.totalco2

-- blood count parameters
, stg3.hematocrit
, stg3.hemoglobin
, stg3.carboxyhemoglobin
, stg3.methemoglobin

-- chemistry
, stg3.chloride
, stg3.calcium
, stg3.temperature
, stg3.potassium
, stg3.sodium
, stg3.lactate
, stg3.glucose

-- ventilation / misc
, stg3.intubated
, stg3.tidalvolume
, stg3.ventilationrate
, stg3.ventilator
, stg3.peep
, stg3.o2flow
, stg3.requiredo2
FROM stg3
WHERE stg3.lastrowfio2 = 1
AND (stg3.specimen = 'ART' OR stg3.specimen_prob > 0.75)
ORDER BY stg3.hadm_id, stg3.charttime;

-- Suggested indexes (optional but strongly recommended)
-- CREATE INDEX IF NOT EXISTS idx_pivoted_bg_art_icustay_charttime
-- ON mimiciii_derived.pivoted_bg_art (icustay_id, charttime);
-- CREATE INDEX IF NOT EXISTS idx_pivoted_bg_art_hadm_charttime
-- ON mimiciii_derived.pivoted_bg_art (hadm_id, charttime);
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