GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction
Fig 3
A detailed graphical representation of GPRuler tool.
The central part of the figure illustrates the two alternative paths that can be followed to reconstruct the GPR rules according to the two possible inputs of GPRuler: the SBML model (green) and the organism name (blue). The green and the blue rectangles connected to each other by dashed arrows show the steps to follow in each path to achieve the core pipeline (orange rectangle), which returns as ultimate outcome the GPR rules. The ten boxes on the top and bottom of the figure represent the exploited data sources used by GPRuler, including both biological databases (white boxes) and the FuzzyWuzzy Python package (gray box), listing which information is retrieved from each of them. Each coloured arrow links each step of the pipeline to the used source and, in particular, to the type of data for which that particular source is queried.