A longitudinal data framework for context-specific genotype-to-phenotype mapping

Molecular assays can resolve clonal structure, but they are expensive and typically sparse in time, whereas phenotypic observations such as imaging can be collected frequently but often are not preserved in the context needed for later interpretation. We present CLONEID, an event-based framework for organizing clone-resolved phenotypic, molecular, and specimen-context records so that genotype-to-phenotype interpretation can be maintained across time. CLONEID links time-stamped Events, assay-specific Perspectives, and reconciled Identities through structured ingestion, provenance-aware retrieval, and reproducible export, complementing upstream clone-calling methods. In a long-term gastric cancer density-selection experiment, CLONEID linked repeated culture events, growth measurements, and late karyotypic profiling within a shared record, supporting longitudinal interpretation of phenotypic adaptation together with underlying chromosomal state.