title: The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents.
abstract: BACKGROUND
  Currently, there are no ontologies capable of describing both the spatial organization of groups of cells and the behaviors of those cells. The lack of a formalized method for describing the spatiality and intrinsic biological behaviors of cells makes it difficult to adequately describe cells, tissues and organs as spatial objects in living tissues, in vitro assays and in computational models of tissues.
  
  
  RESULTS
  We have developed an OWL-2 ontology to describe the intrinsic physical and biological characteristics of cells and tissues. The Cell Behavior Ontology (CBO) provides a basis for describing the spatial and observable behaviors of cells and extracellular components suitable for describing in vivo, in vitro and in silico multicell systems. Using the CBO, a modeler can create a meta-model of a simulation of a biological model and link that meta-model to experiment or simulation results. Annotation of a multicell model and its computational representation, using the CBO, makes the statement of the underlying biology explicit. The formal representation of such biological abstraction facilitates the validation, falsification, discovery, sharing and reuse of both models and experimental data.
  
  
  METHODS
  The CBO, developed using Protégé 4, is available at http://cbo.biocomplexity.indiana.edu/cbo/ and at BioPortal (http://bioportal.bioontology.org/ontologies/CBO).
authors.affiliation: Department of Physics, Biocomplexity Institute, Indiana University, Bloomington, IN 47405, USA.
authors.forename: James P
authors.initials: JP
authors.lastname: Sluka
authors.affiliation: Department of Physics, Biocomplexity Institute, Indiana University, Bloomington, IN 47405, USA.
authors.forename: Abbas
authors.initials: A
authors.lastname: Shirinifard
authors.affiliation: Department of Physics, Biocomplexity Institute, Indiana University, Bloomington, IN 47405, USA.
authors.forename: Maciej
authors.initials: M
authors.lastname: Swat
authors.affiliation: Department of Physics, Biocomplexity Institute, Indiana University, Bloomington, IN 47405, USA.
authors.forename: Alin
authors.initials: A
authors.lastname: Cosmanescu
authors.affiliation: Department of Physics, Biocomplexity Institute, Indiana University, Bloomington, IN 47405, USA.
authors.forename: Randy W
authors.initials: RW
authors.lastname: Heiland
authors.affiliation: Department of Physics, Biocomplexity Institute, Indiana University, Bloomington, IN 47405, USA.
authors.forename: James A
authors.initials: JA
authors.lastname: Glazier
mesh_terms: D064229:Biological Ontologies; D002468:Cell Physiological Phenomena; D003198:Computer Simulation; D008954:Models, Biological
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