Fig. 3

Three example models in the CODA-ML format. To evaluate the utility of the CODA-ML format, three different examples are introduced. a The RTK signaling pathway includes the MAPK / ERK and PI3K / AKT signaling pathways linked to two cancer-related functions. Many molecules in this pathway have molecular modifications or are protein complexes, which requires molecular representation in detail. b Different isoforms originated from the same gene may have different effects to the same function. The mechanisms of the actions of cisplatin and gemcitabine show that drugs may target different isoforms, which highlights that molecular isoforms are essential for precise representation of mechanisms of drug actions. c The mechanism of genistein actions for hypertension was inferred by a previous model in a computational way. This mechanism shows that mechanisms of drug actions particularly, for complex diseases, may involve inter-anatomical relationships as well as intra-anatomy relationships