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

[troojx]

Summary

This PR completes the PostgreSQL implementation of Sepsis-3–related concepts for MIMIC-III, aligning it with the existing BigQuery logic and the Sepsis-3 implementation used in MIMIC-IV.

Specifically, it addresses missing execution steps, adds required pivoted views for SOFA-related metrics, and adapts the MIMIC-IV Sepsis-3 logic to MIMIC-III in PostgreSQL.

Motivation

While working with the PostgreSQL concepts for MIMIC-III, I observed three gaps that affect reproducibility and correctness of Sepsis-3–related analyses:

1. Treatment scripts exist but are not executed
The treatment scripts (e.g., antibiotic exposure and suspicion of infection) are present in the repository but are not invoked in postgres-make-concepts.sql.

2. Missing pivot logic compared to BigQuery implementation
In the BigQuery version, several SOFA-related measurements are explicitly pivoted.
These pivoted views are required for correct SOFA and Sepsis-3 computation, but are currently absent in the PostgreSQL pipeline.

3. Lack of a complete Sepsis-3 implementation for MIMIC-III
MIMIC-IV provides a well-defined Sepsis-3 implementation. This PR adapts that logic to MIMIC-III, ensuring conceptual consistency across datasets.

What this PR adds

1. Execution of missing treatment scripts

The following existing scripts are now explicitly executed as part of the Postgres concepts pipeline:

-- Missing scripts: treatment
\i treatment/abx_prescriptions_list.sql
\i treatment/suspicion_of_infection.sql

2. Addition of SOFA-related pivoted views

Based on the BigQuery implementation, the following pivoted views were manually rewritten in PostgreSQL syntax (automatic conversion was not applicable):

-- New addition: Pivot calculation for SOFA related metrics
\i pivot/pivoted_bg.sql
\i pivot/pivoted_bg_art.sql
\i pivot/pivoted_uo.sql
\i pivot/pivoted_lab.sql
\i pivot/pivoted_gcs.sql

These views are required for downstream SOFA and Sepsis-3 logic.

3. Sepsis-3 logic for MIMIC-III

A PostgreSQL-compatible Sepsis-3 script was implemented for MIMIC-III by adapting the logic used in MIMIC-IV:

-- Sepsis 3 script
\i sepsis/sepsis3.sql

Integration approach

All additions are integrated into the existing pipeline by appending them to the end of postgres-make-concepts.sql, ensuring:

• No changes to existing execution order
• Backward compatibility with current workflows
• A single entry point for generating all required concepts

Verification

• PostgreSQL version: 14.20
• Dataset: MIMIC-III v1.4

All scripts execute successfully in sequence.

Approximate execution time:

• Pivoted SOFA-related views: ~1 minute each
• pivoted_sepsis view: ~550 seconds
• Sepsis-3 script: ~1 minute

Materialized views are created as expected and align with the BigQuery-derived logic.

Impact

This PR improves:

• Reproducibility of Sepsis-3 research using PostgreSQL
• Consistency between MIMIC-III and MIMIC-IV Sepsis definitions
• Parity between PostgreSQL and BigQuery concept implementations

No existing concepts are modified or removed.