Connect my biobank

The Federated Platform is a part of a broader BBMRI-ERIC IT ecosystem, which was set up to be vendor-neutral and must allows different solutions to coexist based on standards for interoperability. This is particularly important for more advanced services such as the federated search or data analysis platform, where we see potential for different competing solutions to be developed and used. The Platform shall support datafication of BBMRI-ERIC biobanks and the Research Infrastructure (RI) as a whole and support our participation in activities such as implementation of the Mission Cancer and European Health Data Space.

The Federated Platform enables member country state’s national strategies and thus support a hierarchical model in federated searches and federated data analyses. It shall enable biomedical research services provisioning at all hierarchical levels i.e. by biobanks, national coordinators and BBMRI-ERIC.

The Federated Platform Strategy was given by BBMRI-ERIC Common Service IT leads in advance of a tender calling for the federated search platform provision. More details can be found on the Federated Platform Strategy page.

Prerequisites for connecting your biobank/collections to the Platform are:

• Collection(s) registered in the BBMRI-ERIC Directory
• Ability to create a virtual machine to run local component software
• Technical support available to the biobank (either local or via the national node)

Steps for getting connected are:

1. Get in touch with the Federated Search Task Force co-chairs
2. Read the BBMRI-ERIC Data Protection Concept and get approval from your Data Security office if it is required by your internal policy
3. Install the local component (see technical details below)
4. Export appropriate data from your system(s)
5. Transform them to standard format – HL7 FHIR or OMOP CDM based on the tool selected
6. Load the harmonized and standardized data to the local component
7. Connect your local component to the central component of the Federated Platform

Installation guide: Demo on the installation of Locator bridgehead

Extract-Transform-Load (ETL) tools for HL7-FHIR:

1. OpenSpecimen ETL to BBMRI-Locator FHIR resources
2. FHIR module
3. a-small-fire

For visibility in BBMRI-ERIC Locator you need to install a Bridgehead (local component for Locator)

• See basic hardware and software requirements at GitHub page

The Federated Platform is supposed to be a sustainable community driven effort currently heading to its wider deployment and maintenance. BBMRI-ERIC Common Service IT supports the integration of the Federated Platform into the IT ecosystem of BBMRI-ERIC, namely by providing integration with Authentication and Authorization Infrastructure (AAI) and Negotiator. 

The BBMRI Federated Search Task Force organised already several informative and technical sessions for the BBMRI-ERIC national nodes and biobanks to increase the knowledge about Federated Platform tools and local components maintainance. This is performed as a so called “train the trainers” system which makes this whole initiative sustainable.

The biobanks do not have to pay anything for the usage of the local component software but need to cover the costs for the technical realisation and data management by themselves. 

1. Date of diagnosis
2. Diagnosis
3. Diagnosis age donor (years)
4. Donor age (years)
5. Sampling date
6. Sample type
7. Sex
8. Storage temperature