Biological Processes Ontology

I developed a formal yet intuitive knowledge model of biological processes and functions that is graphical, for human comprehension, and machine-interpretable, to allow reasoning. The model enables verification of safety and soundness, and querying information that can assist in discovering relationships among processes and structural components that participate in them.

The framework contains a biological ontology which is used as a controlled vocabulary. By mapping the model to Petri Nets - a formal mathematical model, we can simulate modeled systems and analyze them, looking for properties which would be of interest for researchers.

We implemented our framework using the Protege-2000 tool and tested it by representing domains such as Malaria parasites invading host erythrocytes, and protein translation affected by mutations in tRNA. For more information, and to download examples in my framework, click here.