FAIR data retrieval for sensitive clinical research data in Galaxy

BACKGROUND

In clinical research, data have to be accessible and reproducible, but the generated data are becoming larger and analysis complex. Here we propose a platform for Findable, Accessible, Interoperable, and Reusable (FAIR) data access and creating reproducible findings. Standardized access to a major genomic repository, the European Genome-Phenome Archive (EGA), has been achieved with API services like PyEGA3. We aim to provide a FAIR data analysis service in Galaxy by retrieving genomic data from the EGA and provide a generalized "omics" platform for FAIR data analysis.

RESULTS

To demonstrate this, we implemented an end-to-end Galaxy workflow to replicate the findings from an RD-Connect synthetic dataset Beyond the 1 Million Genomes (synB1MG) available from the EGA. We developed the PyEGA3 connector within Galaxy to easily download multiple datasets from the EGA. We added the gene.iobio tool, a diagnostic environment for precision genomics, to Galaxy and demonstrate that it provides a more dynamic and interpretable view for trio analysis results. We developed a Galaxy trio analysis workflow to determine the pathogenic variants from the synB1MG trios using the GEMINI and gene.iobio tool. The complete workflow is available at WorkflowHub, and an associated tutorial was created in the Galaxy Training Network, which helps researchers unfamiliar with Galaxy to run the workflow.

CONCLUSIONS

We showed the feasibility of reusing data from the EGA in Galaxy via PyEGA3 and validated the workflow by rediscovering spiked-in variants in synthetic data. Finally, we improved existing tools in Galaxy and created a workflow for trio analysis to demonstrate the value of FAIR genomics analysis in Galaxy.

Beacon v2 and Beacon networks: A "lingua franca" for federated data discovery in biomedical genomics, and beyond

Beacon is a basic data discovery protocol issued by the Global Alliance for Genomics and Health (GA4GH). The main goal addressed by version 1 of the Beacon protocol was to test the feasibility of broadly sharing human genomic data, through providing simple "yes" or "no" responses to queries about the presence of a given variant in datasets hosted by Beacon providers. The popularity of this concept has fostered the design of a version 2, that better serves real-world requirements and addresses the needs of clinical genomics research and healthcare, as assessed by several contributing projects and organizations. Particularly, rare disease genetics and cancer research will benefit from new case level and genomic variant level requests and the enabling of richer phenotype and clinical queries as well as support for fuzzy searches. Beacon is designed as a "lingua franca" to bridge data collections hosted in software solutions with different and rich interfaces. Beacon version 2 works alongside popular standards like Phenopackets, OMOP, or FHIR, allowing implementing consortia to return matches in beacon responses and provide a handover to their preferred data exchange format. The protocol is being explored by other research domains and is being tested in several international projects.

The Data Use Ontology to streamline responsible access to human biomedical datasets

Human biomedical datasets that are critical for research and clinical studies to benefit human health also often contain sensitive or potentially identifying information of individual participants. Thus, care must be taken when they are processed and made available to comply with ethical and regulatory frameworks and informed consent data conditions. To enable and streamline data access for these biomedical datasets, the Global Alliance for Genomics and Health (GA4GH) Data Use and Researcher Identities (DURI) work stream developed and approved the Data Use Ontology (DUO) standard. DUO is a hierarchical vocabulary of human and machine-readable data use terms that consistently and unambiguously represents a dataset's allowable data uses. DUO has been implemented by major international stakeholders such as the Broad and Sanger Institutes and is currently used in annotation of over 200,000 datasets worldwide. Using DUO in data management and access facilitates researchers' discovery and access of relevant datasets. DUO annotations increase the FAIRness of datasets and support data linkages using common data use profiles when integrating the data for secondary analyses. DUO is implemented in the Web Ontology Language (OWL) and, to increase community awareness and engagement, hosted in an open, centralized GitHub repository. DUO, together with the GA4GH Passport standard, offers a new, efficient, and streamlined data authorization and access framework that has enabled increased sharing of biomedical datasets worldwide.