cumulus-etl 4.0.0

Turns FHIR data into de-identified & aggregated records

Cumulus ETL

Cumulus is an entire healthcare pipeline for population-scale clinical investigations.

Cumulus ETL is an early critical piece of that pipeline.

• It extracts clinical data from your FHIR exports (you can use SMART Fetch to export FHIR from your EHR).
• It transforms that data by anonymizing it and/or running NLP on clinical notes
• It loads that data onto the cloud to be queried by Cumulus Library SQL

Documentation

For guides on installing & using Cumulus ETL, read our documentation.

Example

A simple run of Cumulus ETL might look something like:

docker compose run \
  cumulus-etl \
  s3://my-input-bucket/bulk-export/ \
  s3://my-output-bucket/delta-lakes/ \
  s3://my-phi-bucket/build-and-phi-artifacts/

This line would read ndjson files from the input bucket, drop the result as Delta Lakes into the output bucket, and save some bookkeeping configuration to a build/phi bucket.

Contributing

We love 💖 contributions!

If you have a good suggestion 💡 or found a bug 🐛, read our brief contributors guide for pointers to filing issues and what to expect.

If you're a programmer ⌨ and are looking for a starting place to help, we keep a list of good bite-size issues for first-time contributions.