Bridging the Metadata Gap: A Unified Science Gateway for Plant Research Data Lifecycle

Le résumé fourni par la source

The metadata gap arising from the digital transformation of plant biology lies between the active documentation of laboratory experiences and the FAIR-compliant publication of the structured data contained therein. Although electronic lab notebooks (ELNs) are replacing paper-based lab notebooks,the conversion of these narrative forms of documentation into structured, standards-based databases represents a major barrier to researchers publishing their data. The authors present a science gateway architecture developed for the DataPLANT consortium and the Collaborative Research Centre PlantMicrobeconsortium to bridge the metadata gap using an annotated research context (ARC) as a central FAIR digital object.The distributed hosting model uses the de.NBI Cloud at the University of Tubingen for service orchestration, with resiliency and off-site redundancy provided by the Leibniz Supercomputing Center (LRZ) in Garching. The architecture integrates Keycloak for identity management, eLabFTW for experimentdocumentation, and a high-availability GitLab instance as the versioned backend. We examine the metadata handover lifecycle and the technical design of the middleware harvesting tool, currently under development, which will utilize REST APIs to automatically extract the experimental context from ELNs andconvert it into ISA-standardized Annotated Research Contexts (ARCs). We address challenges in semantic mapping, API-driven synchronization, and data standardization. This approach reduces the manual burden of FAIR-compliant data management and supports long-term sustainability for multi-site research.

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