EHR-TO-CLIF

Overview

This repository is a practical guide to CLIFing—the process of transforming local clinical EHR data into a CLIF.

📚 Key Resources

Resource	Description
Epic UserWeb: CLIF SQL Queries	SQL queries for Epic Caboodle/Clarity to extract CLIF tables (requires Epic UserWeb access)
CLIF-MIMIC	Reference ETL implementation converting MIMIC-IV → CLIF
CLIF Data Dictionary	Official schema definitions and mCIDE vocabularies
CLIF 101	Beginner's guide to working with CLIF data
clifpy	Python package for validation and analysis
CLIF Lighthouse	Interactive QC dashboard

---

Different institutions take different paths to build their CLIF instances. There is no one-size-fits-all solution, as source EHR systems, data availability, and local constraints vary widely.

The goal of this repo is to document how we built our CLIF pipeline, starting from a local EHR and progressing step by step to a CLIF-ready dataset, and to share lessons learned along the way. (we try to share as much as we can)

What This Repository Covers

• The overall pathway from EHR → CLIF
• Design decisions and trade-offs we made
• Mapping strategies for diagnoses, procedures, labs, and ICU concepts
• Common challenges encountered during CLIF implementation
• Practical examples and scripts used in our pipeline

This is not intended to be a strict template, but rather a reference and starting point for other teams building their own CLIF instances.

What This Repository Is Not

• A plug-and-play CLIF solution
• A definitive or “correct” way to build CLIF
• A replacement for official CLIF documentation

Instead, it reflects one real-world implementation and is meant to complement existing CLIF resources.

Intended Audience

• Researchers and engineers working with ICU or clinical EHR data
• Institutions planning to adopt or pilot CLIF
• Teams looking for practical examples beyond high-level specifications

How to Use This Repo

• Review the documented pipeline to understand the full CLIFing process
• Adapt relevant steps to your local data and infrastructure
• Use examples as guidance, not strict requirements

Contributing Your Site's ETL

We encourage sites to share their ETL approaches! To contribute:

1. Create a folder with your site/institution name (e.g., RUSH/, UCMC/)
2. Add your data transformation scripts (censored of any PHI or proprietary details)
3. Include a brief README explaining your EHR source and approach
4. Submit a PR

The more examples we collect, the easier it becomes for new sites to onboard.

Questions?

• Join the #clif-code-ecosystem channel in the CLIF Consortium Slack
• Check the Epic UserWeb thread for Epic-specific discussions
• Review CLIF-MIMIC for a complete reference implementation