Semantic Beacons: a framework to support federated querying over genomic variants and public Knowledge Graphs
Résumé
Comprehensive genomic data exchange is challenging but critical for future research. Beacon API networks, promoted by initiatives like Global Alliance for Genomics and Health (GA4GH), facilitate genomic variation data discovery while preserving privacy and data ownership. However, their use is often limited by the need for costly storage, compute intensive data pre-processing, and periodic updates as genomic knowledge constantly progresses. This work proposes an on-the-fly approach for enriching genomic variants with biological annotations provided by established knowledge bases. It thus reduces the computational load and processing time. We explore integrating open and interoperable life sciences knowledge graphs with sensitive health genomic data discoverable through Beacon APIs. We propose this federated framework as a step towards increasing FAIRness of genomic data.
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