Cumulus is an entire healthcare pipeline for population-scale clinical investigations.
Cumulus ETL is the first critical piece of that pipeline.
- It extracts bulk patient data from your EHR.
- It transforms that data by anonymizing it and running NLP on clinical notes
- It loads that data onto the cloud to be queried by Cumulus Library SQL
For guides on installing & using Cumulus ETL, read our documentation.
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.
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.