SBGN Process Description (SBGN-PD) is an excellent standard for representing metabolic processes with high biochemical accuracy. Its precise depiction of reactions, substrates, and products makes it ideal for detailed modeling of cellular metabolism.
In contrast, SBGN Activity Flow (SBGN-AF) is particularly well-suited for illustrating gene regulatory and signal transduction pathways, where the exact biochemical mechanisms may either be unknown or not crucial to the analysis. This makes it a powerful tool for abstracting and visualizing high-level regulatory interactions.
However, in biology, no process exists in isolation. Metabolism, gene regulation, and signaling are deeply interconnected and constantly influence each other. This interplay becomes especially relevant in constraint-based modeling approaches, such as Flux Balance Analysis (FBA), where Escher maps are often used to visualize metabolic networks. Escher maps resemble SBGN-PD diagrams in structure and can be converted into such representations.
It is common practice to include elements reminiscent of SBGN-AF to enrich these maps with regulatory context. For example, gene-protein-reaction (GPR) associations are frequently represented alongside metabolic reactions. These are often visualized using dashed lines leading to a box containing the GPR logic, providing a sort of “magnification effect”—indicating that each reaction is underpinned by genomic information.
These associations can also be encoded in SBML using the FBC (Flux Balance Constraints) package version 2, which introduces geneProduct and association elements to capture the GPR relationships formally.
Unfortunately, current SBGN standards do not permit mixing SBGN-PD and SBGN-AF elements within a single diagram, which poses a challenge for integrated representations.
It would be highly desirable to develop interactive SBGN-PD diagrams that allow users to dynamically explore this additional layer of regulation. For instance, hovering over a process node could trigger a zoom-like effect, revealing the associated GPRs — thereby connecting biochemical and regulatory information seamlessly and intuitively.
Being able to draw inlays of AF diagrams within or next to PD process nodes and connect them somehow would be a notable step forward.
SBGN Process Description (SBGN-PD) is an excellent standard for representing metabolic processes with high biochemical accuracy. Its precise depiction of reactions, substrates, and products makes it ideal for detailed modeling of cellular metabolism.
In contrast, SBGN Activity Flow (SBGN-AF) is particularly well-suited for illustrating gene regulatory and signal transduction pathways, where the exact biochemical mechanisms may either be unknown or not crucial to the analysis. This makes it a powerful tool for abstracting and visualizing high-level regulatory interactions.
However, in biology, no process exists in isolation. Metabolism, gene regulation, and signaling are deeply interconnected and constantly influence each other. This interplay becomes especially relevant in constraint-based modeling approaches, such as Flux Balance Analysis (FBA), where Escher maps are often used to visualize metabolic networks. Escher maps resemble SBGN-PD diagrams in structure and can be converted into such representations.
It is common practice to include elements reminiscent of SBGN-AF to enrich these maps with regulatory context. For example, gene-protein-reaction (GPR) associations are frequently represented alongside metabolic reactions. These are often visualized using dashed lines leading to a box containing the GPR logic, providing a sort of “magnification effect”—indicating that each reaction is underpinned by genomic information.
These associations can also be encoded in SBML using the FBC (Flux Balance Constraints) package version 2, which introduces
geneProductandassociationelements to capture the GPR relationships formally.Unfortunately, current SBGN standards do not permit mixing SBGN-PD and SBGN-AF elements within a single diagram, which poses a challenge for integrated representations.
It would be highly desirable to develop interactive SBGN-PD diagrams that allow users to dynamically explore this additional layer of regulation. For instance, hovering over a process node could trigger a zoom-like effect, revealing the associated GPRs — thereby connecting biochemical and regulatory information seamlessly and intuitively.
Being able to draw inlays of AF diagrams within or next to PD process nodes and connect them somehow would be a notable step forward.