PlantMDCS: A code-free, modular toolkit for rapid deployment of plant multi-omics databases

The rapid accumulation of plant multi-omics datasets has increased the need for systems that support local data management, analysis, and reuse. However, construction of conventional web-based databases often requires programming expertise and long-term maintenance, limiting its accessibility for small research groups and project-specific datasets. Here, we developed the Plant Multi-omics Database Construction System (PlantMDCS), a locally deployable, user-friendly graphical platform for the construction and management of plant multi-omics databases. PlantMDCS uses a decoupled front-end and back-end architecture. The back end serves as the core engine for data management and computation and is responsible for the storage, integration, and hierarchical association of multi-omics data. Once initialized, the front end supports the complete research workflow, including data import, querying, integrative analysis, and visualization. All operations can be performed without programming, and local resource usage is mainly governed by the disk storage required for user-provided datasets rather than sustained computational overhead. Benchmarking across representative plant datasets from alfalfa, maize, rice, poplar, and wheat showed that PlantMDCS can efficiently construct local database modules from appropriately prepared datasets. Concurrent-access testing defined the stable operating range and scalability limits under local deployment. A publicly accessible PlantMDCS Demonstration Database (PlantMDCS-MOD) demonstrates the deployment of multi-species and multi-omics database entries generated by PlantMDCS. An end-to-end alfalfa transcriptome-metabolome case study further demonstrates the biological applicability of PlantMDCS. PlantMDCS thus provides a practical framework for transforming fragmented file-based plant multi-omics workflows into reusable, locally controlled, database-supported analytical systems.