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Extract FHIR data, Transform with NLP and DEID tools, and then Load FHIR data into a SQL Database for analysis

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smart-on-fhir/cumulus-etl

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Cumulus ETL

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

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.

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Extract FHIR data, Transform with NLP and DEID tools, and then Load FHIR data into a SQL Database for analysis

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