Ten simple rules for creating reusable pathway models for computational analysis and visualization
Fig 2
Use of graphical annotations in the NAD+ metabolism pathway at WikiPathways (wikipathways:WP3644) [62].
Since one of the most common uses of pathway models is data visualization on nodes, nodes must be adequately sized to allow for efficient data visualization. Accounting for this, node size can then be optimized to the overall size and complexity of the pathway model, utilizing a smaller node size for models with many nodes and a larger node size for sparse models. A consistent representation of different molecular types in terms of size and shape is important, for example, using a specific shape for gene products/proteins and another for metabolites. Any nonstandard nodes or entities should be defined in a legend in the model, as well as in the textual description. NAD+, nicotinamide adenine dinucleotide.