diff --git a/README.md b/README.md index 9610842..9263c16 100644 --- a/README.md +++ b/README.md @@ -4,6 +4,19 @@ This repository is a practical guide to **CLIFing**β€”the process of transforming local clinical EHR data into a CLIF. +## πŸ“š Key Resources + +| Resource | Description | +|----------|-------------| +| **[Epic UserWeb: CLIF SQL Queries](https://userweb.epic.com/Thread/136603/CLIF-A-Common-Longitudinal-ICU-data-Format-for-Federated-Cri/)** | SQL queries for Epic Caboodle/Clarity to extract CLIF tables (requires Epic UserWeb access) | +| **[CLIF-MIMIC](https://github.com/Common-Longitudinal-ICU-data-Format/CLIF-MIMIC)** | Reference ETL implementation converting MIMIC-IV β†’ CLIF | +| **[CLIF Data Dictionary](https://github.com/Common-Longitudinal-ICU-data-Format/CLIF)** | Official schema definitions and mCIDE vocabularies | +| **[CLIF 101](https://common-longitudinal-icu-data-format.github.io/CLIF-101/)** | Beginner's guide to working with CLIF data | +| **[clifpy](https://github.com/Common-Longitudinal-ICU-data-Format/clifpy)** | Python package for validation and analysis | +| **[CLIF Lighthouse](https://github.com/Common-Longitudinal-ICU-data-Format/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. @@ -38,3 +51,20 @@ Instead, it reflects **one real-world implementation** and is meant to complemen - 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](https://userweb.epic.com/Thread/136603/) for Epic-specific discussions +- Review [CLIF-MIMIC](https://github.com/Common-Longitudinal-ICU-data-Format/CLIF-MIMIC) for a complete reference implementation