de2Miabis – BBMRI.de → MIABIS on FHIR Transformer

A Python command-line tool that transforms FHIR resources and collection bundles conforming to the BBMRI.de/GBA Implementation Guide into resources conforming to the MIABIS on FHIR Implementation Guide.

Developed as part of BBMRI-ERIC interoperability work.

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Supported Transformations

BBMRI.de Resource	MIABIS on FHIR Profile
Specimen	miabis-sample
Patient	miabis-sample-donor
Condition	miabis-condition
Biobank (Organization)	miabis-biobank
Collection (Organization)	miabis-collection-organization
Observations (BMI, BodyHeight, BodyWeight, TobaccoUse, CauseOfDeath)	miabis-observation

Code mappings handled:

• Material type – BBMRI.de SampleMaterialType → MIABIS miabis-material-type-CS
• Storage temperature – BBMRI.de StorageTemperature → MIABIS miabis-storage-temperature-cs
• Sample diagnosis – BBMRI.de OtherSampleDiagnosis → MIABIS miabis-sample-diagnosis-cs
• Profile URLs – all BBMRI.de StructureDefinition references remapped to MIABIS equivalents
• Extension URLs – StorageTemperature, SampleDiagnosis, and Custodian extensions remapped

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Requirements

• Python 3.8+
• No external dependencies (standard library only)

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Usage

# Transform a single FHIR JSON file
python bbmri_de_to_miabis.py input.json output.json

# Transform all JSON files in a directory
python bbmri_de_to_miabis.py input_dir/ output_dir/

# Print a mapping summary
python bbmri_de_to_miabis.py --summary

# Verbose / debug output
python bbmri_de_to_miabis.py input.json output.json --verbose

If no output path is given for a single file, the result is written to <input_basename>_miabis.json.
If no output directory is given for a directory, results go to <input_dir>_miabis/.

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Project Structure

de2Miabis/
├── bbmri_de_to_miabis.py       # Main transformer script
├── test_bbmri_de_bundle.json   # Example BBMRI.de input bundle
├── test_miabis_output.json     # Example MIABIS on FHIR output bundle
└── README.md

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Links

• BBMRI.de FHIR IG: https://fhir.bbmri.de
• MIABIS on FHIR IG: https://fhir.bbmri-eric.eu
• BBMRI-ERIC: https://www.bbmri-eric.eu
• GitHub: https://github.com/sthanke

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License

This project is developed within BBMRI-ERIC. Please check with the project maintainers for licensing details.