NLM DIR Seminar Schedule

Abstract:

The Systems Biology Graphical Notation (SBGN) provides standardized visual languages for representing complex biological processes, facilitating communication, reproducibility, and model sharing in systems biology. However, generating high-quality SBGN maps from scratch can be challenging, particularly for new users, due to the steep learning curve of advanced editors and the difficulty of translating informal ideas into structured diagrams. To address these challenges, we present a workflow that streamlines SBGN map creation and refinement through three key steps, supporting both Process Description (PD) and Activity Flow (AF) languages. The first step enables automatic conversion of hand-drawn SBGN sketches into SBGN-ML format using large language models with in-context learning. Quick correction of small recognition errors is supported through an interactive interface, while biological identifiers are mapped automatically using an external library. Second, the workflow supports flexible merging and splitting of maps. Digitized maps can be merged with existing ones to create larger networks in incremental steps by identifying nodes and edges with common attributes, or reorganized into smaller components as needed, while respecting existing layouts in both cases. Finally, we introduce layout refinement methods. A user-guided layout algorithm allows sketch-based hints to influence the arrangement of the entire network or selected subgraphs, while a polishing step improves readability by aligning edges orthogonally or diagonally and organizing nodes by functional role (input, output, modifier). Together, these features provide an end-to-end solution for transforming informal sketches into structured, publication-ready SBGN maps, lowering the entry barrier for new users while offering flexible control for experts.