An Ontology for Cellular Processes

States and bioentities. Components of a GRN are macromolecules (e.g., DNAs, RNAs, or proteins), small molecules (e.g., ions, GTP, or ATP), or 

Compartments. Transitions also include transport of molecules between cell compartments. The set of transitions that a state can be involved in is strictly related to its compartment accordingly, a change in the compartment means a change in the state s information context. The state s compartment is a part of the ontology. As the compartments and their vicinity are cell-type dependent, compartmental structure can be modeled as part of the ontology. Cell membranes create an additional complexity because not only can a molecule be located completely inside the membrane, but it may also communicate with both sides of the membrane as part of the events involved in adjacent compartments. So membranes are considered as separate compartments in the ontology. 

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