Schematic representation of a part of the representation generated for BIOMD0000000082. Here, we demonstrate part of the transformation of the specification of the model BIOMD0000000082 (in silico, on the left) into a representation of in vivo phenomena (on the right). Each line represents an explicit assertion we create and by which knowledge that is currently implicit in the SBML code is made explicit in an ontology-based, formal representation. The World of BIOMD0000000082 has, as a part, a Cell (represented by the model's component). The Cell has, as its parts, three species (represented by "GTP", "DRG" and "DRG_GTP"). The reaction "GTP binding with DRG" represents a process that occurs in the World of BIOMD0000000082 and has as input the objects represented by "GTP" and "DRG", and has as output the object represented by "DRG_GTP". The input and output relations for processes are inferred from the SBML list of reactants and products, respectively.
Hoehndorf et al. BMC Systems Biology 2011 5:124 doi:10.1186/1752-0509-5-124