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sql/build_sepsis3.sql

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+-- ------------------------------------------------------------------
+-- Build the Sepsis-3 onset table on a vanilla PostgreSQL MIMIC-III
+-- v1.3 DB.
+--
+-- Usage (assuming you have already restored the MIMIC-III dump into a
+-- database called `mimic` and have the base tables in the `mimiciii`
+-- schema):
+--
+--   psql -d mimic -v ON_ERROR_STOP=1 \
+--        -c 'SET search_path TO mimiciii, public;' \
+--        -f sql/build_sepsis3.sql
+--
+-- Resulting tables created in the current search_path:
+--   echo_data
+--   urine_output
+--   ventilation_classification
+--   ventilation_durations
+--   weight_durations
+--   {dobutamine,dopamine,epinephrine,norepinephrine}_dose
+--   blood_gas_arterial            (all-time PaO2/FiO2)
+--   gcs_all                       (all-time GCS)
+--   sofa_grid, sofa_vs, sofa_gcs, sofa_bili, sofa_cr, sofa_plt,
+--     sofa_pf, sofa_uo, sofa_vaso, sofa_wide, sofa_components
+--                                 (intermediate hourly stages,
+--                                  retained for inspection)
+--   sofa_hourly                   (final hourly SOFA, one row per
+--                                  ICU hour, with 24-h rolling MAX)
+--   antibiotic                    (filtered antibiotic prescriptions)
+--   suspicion_of_infection        (Seymour 2016 abx<>culture pairing)
+--   sepsis3                       (final sepsis-3 onset, one row per
+--                                  ICU stay)
+--
+-- Runtime: expect a few hours on a stock single-node PostgreSQL with
+-- the default `chartevents` and `labevents` indexes.  Most of the
+-- cost is the eight raw-table scans driving the sofa_* staging
+-- tables; each stage prints its progress via psql's default ECHO.
+-- ------------------------------------------------------------------
+
+\set ON_ERROR_STOP on
+
+-- 0. PL/pgSQL shims for BigQuery-style DATETIME_DIFF / _ADD / _SUB
+\i postgres-functions.sql
+
+-- 1. Helpers shared with SAPS-II
+\i echo_data.sql
+\i fluid_balance/urine_output.sql
+\i durations/ventilation_classification.sql
+\i durations/ventilation_durations.sql
+\i durations/weight_durations.sql
+
+-- 2. Vasopressor dose tables (each merges CareVue + MetaVision)
+\i durations/dobutamine_dose.sql
+\i durations/dopamine_dose.sql
+\i durations/epinephrine_dose.sql
+\i durations/norepinephrine_dose.sql
+
+-- 3. All-time pivots feeding hourly SOFA
+\i sepsis/blood_gas_arterial.sql
+\i sepsis/gcs_all.sql
+
+-- 4. Hourly SOFA pipeline (staged temp tables -> sofa_hourly)
+\i sepsis/sofa_hourly.sql
+
+-- 5. Suspicion of infection
+\i sepsis/antibiotic.sql
+\i sepsis/suspicion_of_infection.sql
+
+-- 6. Final onset table
+\i sepsis/sepsis3.sql
+
+\echo 'Sepsis-3 build complete.'
+\echo 'Query results with:'
+\echo '  SELECT icustay_id, suspected_infection_time, sofa_time, sofa_score, sepsis3'
+\echo '    FROM sepsis3 WHERE sepsis3 = TRUE LIMIT 10;'