Cell system ontology: representation for biological pathways
University of Tokyo
2006. 12. 27
301-421, 16:00 PM
Networks of molecular interaction in biological processes reveal different levels of granularities, as well as different levels of abstraction. Along with accumulation of huge amounts of biological pathways, data retrieval and integration become more important than ever. However it is difficult to provide formal and explicit representations which cover diverse biological entities and their relationships. The ontology language is an emerging approach within bioinformatics because it is suitable to clarify semantics and to accurately represent the content of a complex domain. We have developed Cell System Ontology (CSO) to represent diverse pathway types including metabolic pathways, regulatory pathways, signal transduction, and cell-cell interaction. CSO aims to support modeling of pathways, 2) visual representation with graphical properties such as shape, color, and size 3) mathematical simulation, 4) reasoning about the processes such as processing speed and reaction rates of each process, 5) functionality of the pathway such as participants and their roles in the processes, and the results, 6) integration method of other ontologies and databases. In addition, CSO accommodates existing pathway representation: KEGG, SBML, CellML, and BioPAX.
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