A methodological framework for developing bioinformatics databases: a case study on the Boesenbergia rotunda genome...

Comprehensive, well-structured databases are critical for storing, integrating, and analyzing genomics data. This manuscript presents a hybrid methodology combining the traditional Database Development Life Cycle (DDLC) with agile principles to build a comprehensive genome database for Boesenbergia rotunda, known as Fingerroot ginger. Boesenbergia rotunda (L.) Mansf., also recognized as Fingerroot ginger or Chinese keys, is a perennial herb from the Zingiberaceae family in the order Zingiberales. Fingerroot ginger is widely used in Asian cuisine, especially the rhizome, and is recognized for its potent bioactive compounds, including panduratin A, 4-hydroxypanduratin, and cardamonin, which are reported to have notable anti-inflammatory, anti-tumor, and antimicrobial, especially antiviral, effects. The Fingerroot Genome Database incorporates genome, transcriptome, coding sequences, and functional annotations in a relational schema of 27 tables. Using iterative refinement during modular development, we integrated tools such as BLAST+ and JBrowse2 to support sequence search and genome visualization. This case study illustrates how a structured DDLC approach can be combined with Agile-inspired refinement to guide the development of a species-specific bioinformatics database for an underexplored medicinal plant.