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A KGML Translation
Figure 6: An illustration of KGML translation mentioned in Section 2.1. The first and second operations aim to unify the expression of reaction. The third operation aims to eliminate inconsistencies between node types. The Orthology nodes in KGML file are omitted during this translation.
B Data Format
Our dataset is stored in a JSON file. And the hierarchy structure is organized as follows:
The node types include Submap, Macromolecule, Process, Complex, Multimer, Simple Chemical and Others. The Others is the union of several types occurring only in a single database (e.g., Unspecified Entity, Association in Reactome and Transport in Pathbank). Nodes in this type account for  $7\%$  over the whole dataset. The edge types include Catalysis, Consumption, Stimulation, Inhibition, Production, Logic Arc and Belong To, where the Belong To represents edges that were added for Complex node reconstruction mentioned in Section 2.1.