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.
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.
Protege files: Workflow with Malaria + tRNA examples The Petri Net Malaria example in Protege
Examples in formats of different Petri Net tools:
Mobius Malaria example file
TimeNET Malaria example file
DesignCPN Malaria example file tRNA example file
GenomicObjectNet Malaria example file
Woflan Malaria example file tRNA example file
Appendix A: number of process, participants, and relationships used in the tRNA model
Structure of the Biological Process Ontology
The biological queries
More about the Malaria project
Contact person: Mor Peleg, University