BioMedBridges: A prototype federated query interface for information on biosamples, and linking of biosamples and disease terminology to genome

This deliverable finalizes the work on linking biological sample-related information across data infrastructures, data availability levels and information types. A federated system for sample discovery across biobanks is described, and we also report on the latest work on linking disease classification to the genome.

We built a prototype for biobank federation through MIABIS 2.0, which is the de facto standard for biobank data sharing in BBMRI-ERIC infrastructure and has also been adopted by other biobank networks and projects. We have developed a sample-centred biobank federation framework that aims to facilitate sample discovery among biobanks members of a federation. At the moment the software is called “MIABIS Connect” and its main features are:

1. Open-source software framework that can be easily adopted by the biobank and research communities.
2. Allows biobanks keeping their idiosyncratic semantics and at the same time be able to share data using MIABIS semantic. The harmonization process is data model agnostic.
3. Biobank data stays in the biobank. Only the results of queries are fetched from the biobanks to be viewed through the common query interface.
4. Requires a minimum involvement of biobank IT support in order to deploy and maintain the federation framework.

Following on the association of ICD10 codes to genes, we have developed a new approach creating associations to microRNAs. Since their discovery in 1994, miRNAs as a target are gaining attraction in the research community. To our knowledge, no-one has worked on associating miRNAs to ICD10 diagnostic codes before.