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fhir_meds

https://github.com/rvandewater/fhir_meds

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.8%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: rvandewater
  • Language: Python
  • Default Branch: main
  • Size: 70.3 KB
Statistics
  • Stars: 0
  • Watchers: 0
  • Forks: 0
  • Open Issues: 0
  • Releases: 2
Created 8 months ago · Last pushed 8 months ago
Metadata Files
Readme Citation

README.md

MEDS Logo

MEDS on FHIR

PyPI - Version Documentation Status codecov tests code-quality python license PRs contributors DOI

Overview

[!CAUTION] This package is in alpha development. Use at your own risk.

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

```bash pip install fhir2meds

or for local development

pip install -e . ```

Usage

bash 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):

bash PYTHONPATH=src pytest tests/

References

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.

Owner

  • Name: Robin van de Water
  • Login: rvandewater
  • Kind: user
  • Location: Berlin
  • Company: Hasso Plattner Institute

PhD student in Medical Event Prediction at Hasso Plattner Institute in collaboration with the Charité hospital (Berlin)

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
url: "https://github.com/rvandewater/FHIR2MEDS"
title: "FHIR2MEDS ETL (MEDS on FHIR)"
doi: "10.5281/zenodo.16269018"
authors:
  - family-names: "van de Water"
    given-names: "Robin Philippus"
    orcid: "https://orcid.org/0000-0002-2895-4872"
repository-code: "https://github.com/rvandewater/FHIR_MEDS"
date-released: "2025-07-21"
url: "https://github.com/rvandewater/FHIR_MEDS"
license: "MIT"

GitHub Events

Total
  • Release event: 1
  • Public event: 1
  • Push event: 2
  • Create event: 1
Last Year
  • Release event: 1
  • Public event: 1
  • Push event: 2
  • Create event: 1

Dependencies

.github/workflows/code-quality-main.yaml actions
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
  • pre-commit/action v3.0.1 composite
.github/workflows/code-quality-pr.yaml actions
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
  • pre-commit/action v3.0.1 composite
  • trilom/file-changes-action v1.2.4 composite
.github/workflows/python-build.yaml actions
  • actions/checkout v4 composite
  • actions/download-artifact v4 composite
  • actions/setup-python v5 composite
  • actions/upload-artifact v4 composite
  • pypa/gh-action-pypi-publish release/v1 composite
  • sigstore/gh-action-sigstore-python v3.0.0 composite
.github/workflows/tests.yaml actions
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
  • codecov/codecov-action v4.0.1 composite
  • codecov/test-results-action v1 composite
pyproject.toml pypi
  • beautifulsoup4 *
  • fhir.resources >=6.3.0
  • hydra-core *
  • meds ~=0.4.0
  • polars >=1.20.0
  • pyarrow >=12.0.0
  • pyyaml >=6.0
  • requests *