FHIR module

The BBMRI-ERIC FHIR module is a container based application connecting biobanks to other IT tools and services in our ecosystem on a local level.

Goal

The goal of this project is to create a highly customizable data integration tool for biobanks that are a part of BBMRI-ERIC. This tool should support ETL processes by providing the following functionality:

• Data harmonization to HL7 FHIR
  • HARMONIZATION for BBMRI.de profile - currently used by BBMRI-ERIC Locator
  • HARMONIZATION for MIABIS on FHIR profile - FHIR profile representing latest MIABIS version (MIABIS Core 3.0 + Individual-level sample components)
• Data quality validation - validates the provided files and mappings - see Deployment
• Reporting and monitoring (coming soon)

State

Supports syncing of patients and their samples between a Blaze FHIR store and a repository of XML or CSV files stored on a regular filesystem. This application Transforms data into the two FHIR profiles, BBMRI.de and MIABIS on FHIR, as mentioned above. Each representation is stored in an independent Blaze FHIR store. MIABIS on FHIR representation serves as a pilot use-case of the newly created profile.

Currently, the XML files must have the same structure as this test file. This module cannot work with different types of files at the same time, so the records needs to be in either XML or CSV format, not both.

Contents of provided record file(s)

In order to successfully transform data about patients and samples, the users need to provide this data:

• patient_data:
  • (pseudo)-anonymized ID of a donor
  • donor_birthdate
  • gender
• sample_data:
  • (pseudo)-anonymized ID of the sample
  • material type
  • • diagnosis_datetime - date that the diagnosis was first observed (optional but recommended for better findability in Locator)
  • storage temperature - (optional but recommended for better findability in Locator)
  • ICD10 diagnosis code
  • new (or already provided) attribute, which specifies to which collection this sample belongs to

Quick Start

Docker

Prerequisites:

• Docker engine v24.0.0
• Docker compose v2.20

To spin up an instance of the FHIR module along with Blaze, clone the repository and run the following command:

docker compose --profile dev up -d

For additional information about deployment, refer to the Deployment documentation.

Workflow

At the start, the FHIR module syncs the provided records - Transforms the provided records into BBMRI.de and MIABIS on FHIR representations and uploads them to the Blaze FHIR store respectively.

The FHIR module periodically - every week - syncs the Blaze store with the records currently present. Only new patients/samples are uploaded.

Additionally, after initial upload, users can manually start the sync of BBMRI.de or MIABIS on FHIR profile representation using the commands:

docker exec fhir-module curl -X POST http://127.0.0.1:5000/sync

for syncing the BBMRI.de representation.

docker exec fhir-module curl -X POST http://127.0.0.1:5000/miabis-sync

for syncing the MIABIS on FHIR representation.

Users can also delete all of the records currently present in the FHIR store, again either BBMRI.de or MIABIS on FHIR representation using the commands:

docker exec fhir-module curl -X POST http://127.0.0.1:5000/delete

for deleting data representing the BBMRI.de.

docker exec fhir-module curl -X POST http://127.0.0.1:5000/miabis-delete

for deleting data representing the MIABIS on FHIR.

Contributing

Because the FHIR module is an open source software pull requests are of course welcome! For further information, please read our contributing guidelines!

Found a security vulnerability? Please refer to our security policy.

For instructions on how to set up the development environment, refer to the corresponding chapter.

License

Copyright 2023 BBMRI community.

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an " AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.