clifpy 0.5.0

A Python package for working with CLIF EHR data

clifpy - Python Client for CLIF

Transform critical care data into actionable insights

Documentation | Quick Start | CLIF Website

Standardized framework for critical care data analysis and research

CLIFpy is the official Python implementation for working with CLIF (Common Longitudinal ICU data Format) data. Transform heterogeneous ICU data into standardized, analysis-ready datasets with built-in validation, clinical calculations, and powerful data manipulation tools.

Key Features

• 📊 Comprehensive CLIF Support: Full implementation of all CLIF 2.0 tables with automatic schema validation
• 🏥 Clinical Calculations: Built-in SOFA scores, comorbidity indices, and other ICU-specific metrics
• 💊 Smart Unit Conversion: Automatically standardize medication dosages across different unit systems
• 🔗 Encounter Stitching: Link related ICU stays within configurable time windows
• ⚡ High Performance: Leverages DuckDB and Polars for efficient processing of large datasets
• 🌍 Timezone Aware: Proper timestamp handling across different healthcare systems
• 📈 Wide Format Support: Transform longitudinal data into hourly resolution for analysis
• ✅ Data Quality Assessment Framework: Comprehensive assessment of conformance, completeness, and plausibility across all CLIF 2.1 Beta tables

Installation

pip install clifpy

Quick Example

from clifpy import ClifOrchestrator

# Load and validate CLIF data
orchestrator = ClifOrchestrator(
    data_directory='/path/to/clif/data',
    timezone='US/Eastern'
)

# Validate all tables against CLIF schemas
orchestrator.validate_all()

# Access individual tables
vitals = orchestrator.vitals.df
labs = orchestrator.labs.df

# Advanced features
wide_df = orchestrator.create_wide_dataset()  # Hourly resolution data
sofa_scores = orchestrator.compute_sofa_scores()  # Calculate SOFA scores

Development

CLIFpy uses uv for fast, reliable dependency management.

Quick Setup

1. Install uv:

   curl -LsSf https://astral.sh/uv/install.sh | sh
   

2. Clone and install:

   git clone https://github.com/Common-Longitudinal-ICU-data-Format/CLIFpy.git
   cd CLIFpy
   uv sync
   

3. Run tests:

   uv run pytest
   

Feature Contributors

Feature	Coder	Clinician	Status
SOFA Score Computation	Kaveri Chhikara	Will Parker	Published
Respiratory Support Waterfall	Kaveri Chhikara	Nick Ingraham	Published
Presumed Infection and ASE	Vaishvik Chaudhari	Kevin Buell	Published
Cumulative Dose Calculation	Zewei (Whiskey) Liao		Future Feature
Lab Conversion Units	Dema Therese	Cathy Gao	In Progress
CRRT Waterfall	Kaveri Chhikara	Shan Guleria, Jay Koyner	Future Feature
Medication Unit Conversion	Zewei (Whiskey) Liao		Published
Data Quality Assessment	Dema Therese		Published
Intubation Extubation	Vaishvik Chaudhari		In Progress

Links & Resources

• 📚 Full Documentation
• 🏥 CLIF Specification
• 🐛 Issue Tracker
• 📦 PyPI Package