Fig. 5

The BpForms-BcForms toolkit can help modelers refine, expand, and compose global intracellular networks. For example, we used BpForms to systematically identify ways to improve and expand the Kholodenko model of MAPK signaling to capture signaling under a broader range of conditions (a, gray) by using BpForms to capture the semantic meaning of each species (a, red), identify missing protein states (b, blue), identify other models that represent similar proteins which could be composed with the Kholodenko model (c, yellow) which could reveal additional missing combinations of species (c, green), and identify element imbalances which indicate missing metabolites which could facilitate composition with metabolic models (d). Together, this could enable a substantially more comprehensive and predictive model that can explain eukaryotic signaling under a broader range of disease conditions (e)