Replication package for: "Enhancing Interoperability of HL7 Resources Using Namespaces in Graph Databases"

This repository is used as a replication package for the work on "Enhancing Interoperability of HL7 Resources Using Namespaces in Graph Databases".

The project itself is configured as a Maven Java project using Maven 3.8.6 in combination with OpenJDK 11. The main entrypoint of the project is the Neo4jOnFhirMain class. Executing this class will read data from a hapi fhir server and will store it in a Neo4j graph database hosted on localhost:7687.

Requirements

Hapi Fhir Server

It is necessary to have a running Hapi FHIR Server (we used version: 6.2.2) with FHIR Version 4.0.1, which contains a list of patient and AuditEvent data. The data that we used can be found as JSON in the folder /data (cf. patients.json and audit_events.json). The data can be imported using the following command:

curl -X POST --location "http://serverBaseURL/fhir/" \
    -H "Content-Type: application/fhir+json" \
    -d @foldername/patients.json

Neo4j database

A running Neo4j database setup is required in order to store the data. The following docker-compose file could be used to create a running instance:

version: '2'
services:
  db:
    image: neo4j:4.2.19-community
    ports:
      - 7474:7474
      - 7687:7687
    volumes:
      - "localpath/data:/data"
      - "localpath/conf:/var/lib/neo4j/conf"
      - "localpath/plugins:/var/lib/neo4j/plugins"

Please make sure, that both localpath/conf and localphat/plugins need to include a configuration for CyFHIR. The folder can be copied from the data folder using the folders: conf and plugins.

Importing the data using CyFHIR can be done using the following command and replace <json_string> with the content of the file data/patients_filtered.json.

CALL cyfhir.bundle.load('<json_string>')

Note: For our example we used two separate Neo4j database instances, for storing FHIR resources using CyFHIR and our namespace approach to avoid conflicts.

Contributing

First make sure to read our general contribution guidelines.

License

This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this file, You can obtain one at https://mozilla.org/MPL/2.0/.

Files contained in the data/plugins folder are third party apps and may be distributed under different license:

CyFHIR.jar: GPL-3.0
apoc-4.2.0.10-all.jar: Apache-2.0

Research

If you are going to use this project as part of a research paper, we would ask you to reference this project by citing it.