Ziying Yang - Phenopackets for curated repository data over Beacon v2 Progenetix database
Channel: Biocuration Conference 2023
Date: 2023-06-21

*Session:* April 25 - Applications 2 - 03

*Abstract:* Many data repositories such as NCBI GEO contain a vast amount of annotations and metadata from human "omics" experiments, frequently in semi-structured documents accessible through the resource's API. Here, the use of phenopackets, a flexible schema which can represent clinical data for any kind of human disease, over a standardized API such as Beacon v2 will provide major improvements for data harmonization, FAIRification and empowering of federated data analysis strategies.  Progenetix (progenetix.org) is a curated oncogenomic resource with a focus on copy number variation (CNV) profiling. It presently contains data for more than 140,000 hybridization or NGS based experiments derived from a over 1000 publications as well as resources and projects such as GEO, TCGA or cBioportal. All samples are annotated for biological and procedural metadata, e.g. their corresponding resource identifiers, publication ids, NCIt, UBERON and ICD-O codes and cellosaurus ids, where applicable, and additionally for a core set of biological and clinical data. This curated data with its reasonably large content of data from identifier-tagged, public repository linked samples provides an interesting test case for representation of common "omics" metadata as phenopackets documents delivered over the Beacon v2 API.   The Progenetix Beacon+ API recently introduced a "phenopackets" response format (PXF) in expansion of the Beacon v2 default model's entry types. For "record"-level granularity (i.e. document delivery upon a Beacon request) phenopackets are generated ad hoc from Beacon defaults using through the bycon package driving the Progenetix API. Since Beacon v2 schemas for biosamples and individuals have been designed to closely align with the Phenopackets v2 specifications, necessary remappings are of limited complexity. Here, current efforts are aimed at the integration of emerging tools from the Phenopackets ecosystem especially for compliance testing. We have selected example usage scenarios involving common data repositories with curated data represented in Progentix. Based on these use cases, we tested and compared the Beacon+ Phenopackets prototype towards Phenopackets v2 compliance. For this purpose, we iteratively adjust the Beacon+ PXF implementation towards increasing compliance, implement a prototype of a service to extract Phenopackets from Beacon+ Phenopackets responses, and evaluate the implementation of alternative (i.e. non-Beacon) REST APIs for such Phenopackets responses. Based on our implementation of a Beacon API based, PXF formatted representation of repository-derived, curated genomic and metadata we propose a more general adoption of such a scenario. Here, an extensive (multi-10k) demonstrator project which would extend the scope beyond Progenetix data types could showcase usages scenarios and directly support diverse analysis projects, with direct value for the wider "-omics" communities. A future scenario would include direct GA4GH standards integration (Phenopackets, Beacon, service info etc.) to resource providers using the demonstrated benefit from the demonstrator cases.