Simplified class structure and mapping from KGML to BioPAX. The figure shows the raw mapping of KGML to BioPAX class instances. The type attribute of each entry determines how it is translated (see Table 1). Reactions that are catalyzed by enzymes are translated to Catalysis, whereas non-catalyzed reactions are translated directly to BiochemicalReactions. Relations are translated differently, depending on their subtype, the participating entities and the chosen BioPAX level (see Table 2). To keep the clarity, the figure does not include the information that in BioPAX Level 2, control and conversion inherit from physicalInteraction. Furthermore, a Catalysis consists of two elements: a Controller and a Controlled element. For our purposes, Controller is always an enzyme and Controlled is a BiochemicalReaction. Similarly, KGML relations may be translated to a Control element that regulates either a Conversion or TemplateReaction.
Wrzodek et al. BMC Systems Biology 2013 7:15 doi:10.1186/1752-0509-7-15