COSMOS: A FAIR-aligned infrastructure for clinical trial data validation, warehousing, and interactive discovery

1.SummaryThe Clinical Omics System for Metadata and Outcome Storage (COSMOS) is an open-source, FAIR- and GCP aligned clinical trial unit (CTU) infrastructure designed to streamline the transition of academic clinical and multi-omic trial datasets into curated, analysis-ready repositories within Secure Data Environments (SDEs). By integrating an automated Data Quality and Data Validation (DQ&DV) "Trust Layer" with a relational Structured Query Language (SQL) schema, COSMOS enables programmatic and interactive data access via R Shiny applications. Dynamic integration of omics and clinical data is achieved through analytical data structures (e.g. ExpressionSet objects) linked via relational database identifiers. This lowers technical barriers for researchers and promotes governed data reuse and secondary discovery. Availability and ImplementationCOSMOS is freely available under the GPL-3.0 license at https://github.com/at2e19/SCTU_COSMOS_DQDV_Shiny Supplementary information: Supplementary data are available at Bioinformatics online.