Modeling biological processes using Workflow and Petri Net models

Type of publication: submitted to Bioinformatics

Reference: Mor Peleg, Iwei Yeh, and Russ B. Altman. Modeling biological processes using Workflow and Petri Net models

Abstract
Motivation: We developed a formal yet intuitive knowledge model of biological processes and functions that is both graphical, for human comprehension, and machine-interpretable, to allow reasoning. The model enables verification of safety and soundness, and supports queries that can assist in discovering relationships among processes and structural components that participate in them. Our model bridges the gap between high-level physiological processes or metabolic pathways and molecular-level functions.
Results: We assessed eleven process models that were developed in the fields of software engineering, business, and biology, with respect to their appropriateness for representing biological processes. We found the most appropriate model to be a Workflow model that can model the nesting and ordering of processes, the structural components that participate in the processes, and the roles that they play. In addition, the Workflow model maps to Petri Nets, which allow verification of properties of modeled systems. We extended the Workflow model with elements that are relevant to biological processes and incorporated the TAMBIS ontology as a controlled vocabulary of biological terms. We implemented the ontology using the Protégé-2000 tool and composed queries, falling into five general classes, which can aid discovering relationships among processes and structural components. We used reachability analysis to answer queries that relate to dynamic aspects of the model. We tested our model by representing Malaria parasites invading host erythrocytes.