MIABIS on FHIR — Transaction Bundle Generator & Validator

Python tools for generating and validating FHIR R4 transaction bundles conforming to the MIABIS on FHIR Implementation Guide developed by BBMRI-ERIC.

Overview

This project provides two scripts:

1. generate-miabis-bundle.py — generates synthetic biobank datasets for testing, development, and validation of MIABIS on FHIR endpoints.
2. validate-miabis.py — validates generated bundles against the latest MIABIS on FHIR IG using the HL7 FHIR Validator.

Generated bundles include the full MIABIS resource hierarchy — from juristic persons and biobanks down to individual donor specimens and observations.

Generated Resources

FHIR Resource	MIABIS Concept
Organization (Juristic Person)	Parent legal entity
Organization (Biobank)	Biobank facility
Organization (Network Organization)	Network coordinating entity
Group (Network)	Biobank network membership
Organization (Collection Organization)	Collection metadata
Group (Collection)	Sample collection with characteristics
Patient	Sample donor
Condition	ICD-10 diagnosis
Specimen	Biological sample
DiagnosticReport	Pathology report
Observation	Sample-level diagnosis

Requirements

• Python 3.8+ (no external dependencies needed for generation)
• For validation: Java 17+, Git, Node.js 18+ (details in VALIDATION-GUIDE.md)

Installation

git clone https://github.com/sthanke/MiabisonFHIR_Generator.git
cd MiabisonFHIR_Generator

Quick Start

# 1. Generate a bundle (saved to bundles/ by default)
python generate-miabis-bundle.py --donors 10

# 2. Validate it
python validate-miabis.py

Generating Bundles

python generate-miabis-bundle.py --donors 10
python generate-miabis-bundle.py --donors 50 --biobanks 3 --collections 5
python generate-miabis-bundle.py --donors 100 --output my-bundle.json --seed 42

Generated files are saved to the bundles/ folder by default. Use --output to write to a custom path instead.

Argument	Required	Default	Description
--donors	Yes	—	Number of sample donors to generate
--biobanks	No	1	Number of biobanks
--collections	No	1	Number of collections
--output	No	bundles/miabis-bundle-<N>donors.json	Output file path
--seed	No	random	Random seed for reproducibility

Validating Bundles

See VALIDATION-GUIDE.md for prerequisites, usage, output format, and troubleshooting.

Project Structure

MiabisonFHIR_Generator/
  generate-miabis-bundle.py   # Bundle generator
  validate-miabis.py          # Batch validation script
  bundles/                    # Generated bundles (default output)
  miabis-validation/          # Created by validator (IG clone, reports)
  VALIDATION-GUIDE.md         # Detailed validation documentation
  README.md
  LICENSE

Resources

• MIABIS on FHIR IG
• BBMRI-ERIC
• BBMRI-ERIC Directory

License

This project is released under the MIT License.

Author

Developed by Sten Hanke for BBMRI-ERIC.