Biological Processes Ontology

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.

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 of Haifa