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  MeDaX Pipeline v1.0.0 Stable

  gebhardtt released this 2025-04-24 15:37:50 +02:00 | 0 commits to main since this release

  Release Notes - MeDaX Pipeline v1.0.0 (Initial Release)

  Overview

  We are pleased to announce the first release of our MeDaX pipeline, enabling seamless transformation of hospital FHIR data into a Neo4j graph database, thereby enabling innovative medical data exploration at german Data Integration Centres. This pipeline facilitates:

  • Local setup for controlled data handling
  • Efficient data exploration and analysis across connected healthcare data
  • Improved query capabilities for complex healthcare relationships

  Key Features

  Easy Deployment

  • Containerised setup using Docker Compose for straightforward deployment and configuration
  • Flexible configuration options for connecting to any FHIR server through customisable URL and proxy settings
  • Built-in support for Open Access HAPI FHIR server, enabling immediate testing and validation
  • Simple environment variable configuration through .env file

  Data Processing

  • Validated with real hospital data, ensuring production readiness
  • Implemented property convolution and reference path reduction for efficient graph size reduction
  • Manually curated graph schema to enable semantic enrichment with ontological information, currently using BioLink (BioCypher default)
  • Automated schema extension for unspecified input data to maintain compatibility with evolving FHIR resources
  • Batching of input data to process large-scale data sets
  • Support for patient-centric data retrieval using FHIR's $everything operation

  Extensibility

  • Developed using BioCypher framework, enabling modular architecture
  • Support for additional data source adapters, allowing future expansion to different resources
  • Flexible architecture consists of:
    1. FHIR Import module for data retrieval
    2. Reference Processor for relationship management
    3. Property convolution for complexity reduction
    4. BioCypher Adapter for Neo4j integration

  Installation & Usage

  For detailed installation instructions and information how to cite this work, please refer to the README document included in the repository. Basic setup involves:

  1. Clone the repository
  2. Configure the environment variables
  3. Run docker compose up --build
  4. Access Neo4j at http://localhost:8080/

  Known Issues and Limitations

  Performance Considerations

  • Processing large hospital datasets requires significant computational resources and time due to data complexity
  • Complete pipeline restart required when modifying graph reduction parameters
  • Initial load time may be extensive for large datasets

  User Interface

  • Currently limited to standard Neo4j browser interface
  • Default UI may not be optimal for specialised healthcare use cases

  Technical Requirements

  • Docker and Docker Compose
  • Sufficient storage and computational resources for processing FHIR datasets
    • Currently the memory is the bottleneck, 12GB RAM recommended for a batch size of 200
  • Network access to FHIR server

  Next Steps

  We are actively working on:

  • Testing large-scale data sets
  • Integrating fitting visualisation interfaces
  • Implementing incremental update capability
  • Integration with BRO (Biomedical Resource Ontology) through curated schema mapping for standardised terminology
  • Performance optimisations for handling larger datasets

  Feedback and Contributions

  We welcome feedback, bug reports, and contributions! Please submit issues and pull requests through our repository.

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  © 2025 MeDaX Project Team | Released under MIT License

  Downloads

  • Source Code (ZIP)
  • Source Code (TAR.GZ)