fhir2meds 0.1.0

MEDS on FHIR

Overview

MEDS on FHIR is a Python package for converting HL7 FHIR (v4/v5) resources into the MEDS sharded Parquet format. It supports scalable, schema-validated event extraction and is designed for research and interoperability projects. This project is in its early stages and has been tested mainly with the MIMIC-IV FHIR demo.

Features

• Parses and processes all MEDS-compatible FHIR resource types (v4/v5) (tested with MIMIC-IV FHIR demo)
• Robust mapping from FHIR Observation to MEDS event schema
• Handles patient ID resolution and vocabulary mapping
• Outputs sharded Parquet files, validated against the MEDS schema
• Extensible: add mapping for new FHIR resource types easily
• Comprehensive test suite for FHIR resource parsing

Installation

pip install fhir2meds
# or for local development
pip install -e .

Usage

fhir2meds raw_input_dir=mimic-fhir root_output_dir=example_output ++overwrite=true ++verbose=true

• raw_input_dir: Directory containing FHIR .ndjson/.json files (e.g., MIMIC-IV FHIR demo)
• output_dir: Output directory for MEDS Parquet shards
• max_observations: (Optional) Limit number of observations for debugging
• overwrite: (Optional) Overwrite existing output directory
• verbose: (Optional) Enable verbose logging
• do_download: (Optional) Download MIMIC-IV FHIR demo dataset automatically (to be tested)

Testing

Run the test suite (requires pytest):

PYTHONPATH=src pytest tests/

References

• HL7 FHIR Resource List
• MIMIC-IV FHIR Demo
• MEDS Format & Schema
• ETL_MEDS_Template R4 Resource List: https://hl7.org/fhir/R4/resourcelist.html

License

This project is licensed under the MIT License. See the LICENSE file for details.

Contributing

Pull requests are welcome! For major changes, please open an issue first to discuss what you would like to change.