Home
Softono

Fhir Data Pipes

Open source Apache-2.0 Jupyter Notebook
Website GitHub
217
Stars
121
Forks
144
Issues
23
Watchers
3 months
Last Commit
Data Pipelines & ETL Health & Fitness

 About Fhir Data Pipes

A collection of tools for extracting FHIR resources and analytics services on top of that data.

Platforms

Web Self-hosted

Languages

Jupyter Notebook

Links

Website Source Code

Need Help Installing Fhir Data Pipes?

We provide expert installation service for this software. Our team will install, configure, and secure Fhir Data Pipes on your server. plans start at just $30.

Hire an Expert
Published by
ohs-foundation
Visit View Profile

Fhir Data Pipes

View on GitHub

Build Status codecov

What is this?

This repository includes pipelines to transform data from a FHIR server (like HAPI, GCP FHIR store, or even OpenMRS) using the FHIR format into a data warehouse based on Apache Parquet files, or another FHIR server. There is also a query library in Python to make working with FHIR-based data warehouses simpler.

These tools are intended to be generic and eventually work with any FHIR-based data source and data warehouse. Here is the list of main directories with a brief description of their content:

  • pipelines/ *START HERE*: Batch pipelines to transform data from a FHIR-based source to an analytics-friendly data warehouse or another FHIR store.

  • docker/: Docker configurations for various servers/pipelines.

  • doc/: Documentation for project contributors. See the pipelines README and wiki for usage documentation.

  • utils/: Various artifacts for setting up an initial database, running pipelines, etc.

  • dwh/: Query library for working with distributed FHIR-based data warehouses.

  • bunsen/: A fork of a subset of the Bunsen project which is used to transform FHIR JSON resources to Avro records with SQL-on-FHIR schema.

  • e2e-tests/: Scripts for testing pipelines end-to-end.

NOTE: This was originally started as a collaboration between Google and the OpenMRS community.

Contributions

This is an open-source project and we welcome contributions. Our development process is also open. We use GitHub issues and review processes. If you are working on a feature or an issue, please comment on that GitHub issue to communicate with other developers. It would also be great to attend our weekly developers' calls on Tuesdays; here are the details: