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Background

Building a functional simulation of cells, a tissue, organ or even an entire organism requires an unprecedented effort to fuse techniques derived from biology, chemistry, physics, computer science and information science. Developing models that can be explored using a range of simulation techniques requires a common language capable of describing heterogeneous features and behaviors at various length-scales ranging from molecule to organism. While languages exist for some necessary subareas (e.g. cell physiology, molecular dynamics, and systems biology), many researchers still use ad-hoc formats and vocabulary to describe cell-based multi-cell models (e.g. Cellular Potts Models, Center Models, FEM).

The creation of the Cell Behavior Ontology is an essential first step in providing a universally agreed upon means to describe cell behaviors and consequently (in the longer term) achieve a standardization level similar to the one that the Systems Biology community has achieved with SBML, CellML and the Foundational Model of Anatomy. Just as applications conforming to SBML or CellML can share models encoded in the two standards, so applications conforming to the CBO derived standards (like the proposed Cell Behavior Model Specification Language CBMSL) will achieve similar capacity for model sharing.

From a practical point of view, an ontology is a logical structure that provides a formal description of concepts within a particular domain. An ontology is often a hierarchy of terms with agreed meanings and sets of subterms and modifiers that can apply to each term. Ontologies are unglamorous and tedious to develop, but are crucial to the development of a shareable representations in a particular subject areas. In some cases an ontology has revolutionized a scientific discipline. For example, in genomics, ontologies like the Gene Ontology (GO) allow the hundreds of programs which process biological sequence information to communicate with each other seamlessly—the output of any program serving as the input for another.