Modelling biological processes using workflow and Petri Net models.

@article{citeulike:2295299, abstract = {MOTIVATION: Biological processes can be considered at many levels of detail, ranging from atomic mechanism to general processes such as cell division, cell adhesion or cell invasion. The experimental study of protein function and gene regulation typically provides information at many levels. The representation of hierarchical process knowledge in biology is therefore a major challenge for bioinformatics. To represent high-level processes in the context of their component functions, we have developed a graphical knowledge model for biological processes that supports methods for qualitative reasoning. RESULTS: We assessed eleven diverse models that were developed in the fields of software engineering, business, and biology, to evaluate their suitability for representing and simulating biological processes. Based on this assessment, we combined the best aspects of two models: Workflow/Petri Net and a biological concept model. The Workflow model can represent nesting and ordering of processes, the structural components that participate in the processes, and the roles that they play. It also maps to Petri Nets, which allow verification of formal properties and qualitative simulation. The biological concept model, TAMBIS, provides a framework for describing biological entities that can be mapped to the workflow model. We tested our model by representing malaria parasites invading host erythrocytes, and composed queries, in five general classes, to discover relationships among processes and structural components. We used reachability analysis to answer queries about the dynamic aspects of the model. AVAILABILITY: The model is available at http://smi.stanford.edu/projects/helix/pubs/process-model/.}, address = {Stanford Medical Informatics, Stanford University, CA 94305, USA. peleg@smi.stanford.edu}, author = {Peleg, M. and Yeh, I. and Altman, R. B. }, citeulike-article-id = {2295299}, issn = {1367-4803}, journal = {Bioinformatics}, keywords = {biology, modeling, net, petri, workflow}, month = {June}, number = {6}, pages = {825--837}, posted-at = {2008-01-27 19:38:01}, priority = {2}, title = {Modelling biological processes using workflow and Petri Net models.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/12075018}, volume = {18}, year = {2002} }

TY - JOUR ID - citeulike:2295299 L3 - citeulike-article-id:2295299 TI - Modelling biological processes using workflow and Petri Net models. JF - Bioinformatics VL - 18 IS - 6 SP - 825 EP - 837 AD - Stanford Medical Informatics, Stanford University, CA 94305, USA. peleg@smi.stanford.edu SN - 1367-4803 N2 - MOTIVATION: Biological processes can be considered at many levels of detail, ranging from atomic mechanism to general processes such as cell division, cell adhesion or cell invasion. The experimental study of protein function and gene regulation typically provides information at many levels. The representation of hierarchical process knowledge in biology is therefore a major challenge for bioinformatics. To represent high-level processes in the context of their component functions, we have developed a graphical knowledge model for biological processes that supports methods for qualitative reasoning. RESULTS: We assessed eleven diverse models that were developed in the fields of software engineering, business, and biology, to evaluate their suitability for representing and simulating biological processes. Based on this assessment, we combined the best aspects of two models: Workflow/Petri Net and a biological concept model. The Workflow model can represent nesting and ordering of processes, the structural components that participate in the processes, and the roles that they play. It also maps to Petri Nets, which allow verification of formal properties and qualitative simulation. The biological concept model, TAMBIS, provides a framework for describing biological entities that can be mapped to the workflow model. We tested our model by representing malaria parasites invading host erythrocytes, and composed queries, in five general classes, to discover relationships among processes and structural components. We used reachability analysis to answer queries about the dynamic aspects of the model. AVAILABILITY: The model is available at http://smi.stanford.edu/projects/helix/pubs/process-model/. KW - biology KW - modeling KW - net KW - petri KW - workflow AU - Peleg, M AU - Yeh, I AU - Altman, RB PY - 2002/06// UR - http://view.ncbi.nlm.nih.gov/pubmed/12075018 ER -