Our framework for modeling biological processes is based on the Workflow model of the Workflow Management Coalition and incorporates the TAMBIS ontology as a biological controlled vocabulary. We added other elements that are relevant to biological systems: cellular location information for process participants and the types of evidence that support facts in the knowledge base. We augmented the Workflow model with elements taken from Object-Process Methodology, to create a graphical representation of four relationship types that occur between a process and the structural components that participate in it (i.e., catalysts, substrates, products, and inhibitors).
We implemented our framework using the Protege-2000 tool and tested it by representing Malaria parasites invading host erythrocytes. Using Protege’s axiom language, we composed queries that can aid discovering relationships among processes and structural components. We used reachability analysis on Petri Nets that were manually converted from the Workflow model to answer queries that relate to dynamic aspects.
Notes:
1) In order to view our Protege ontologies, you need to download
Protege
first.
2) All of the projects should be placed in one directory since they
refer to each other.
3) If you use our model, please reference our publication: Peleg M,
Yeh I, Altman RB. Modeling biological processes using Workflow and Petri
Net models. Bioinformatics, in press 2002.
4) We ask that any extension of this model will be made available to
us.
Biological Process ontology version 1 in Protege + Malaria example (CLIPS version, suitable for creating and viewing guidelines in Protege)
The Petri Net Malaria example in Protege
The
Petri Net Malaria example for Woflan (verifiaction)
The tRNA example in Protege + our Process Model version 2
The tRNA example Petri Nets in Design CPN tool for simulation
The
tRNA example Petri Nets for Woflan verification tool
Appendix A: number of process, participants, and relationships used in the tRNA model
Structure of the Biological Process Ontology
More about the Malaria project
Contact person: Mor Peleg,
Stanford Medical Informatics, Stanford University