Abstract
Motivation: 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.Availability and implementation: The CBO, developed using Protégé 4, is available at http://cbo.biocomplexity.indiana.edu/cbo/ and at BioPortal (http://bioportal.bioontology.org/ontologies/CBO).Contact: jsluka@indiana.edu or Glazier@indiana.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Highlights
All biological research requires the use of abstract models, currently no standard method exists for describing the biological content of microscope images of tissues, in vitro experiments or in silico simulations of the tissue dynamics of multicellular systems
We describe the spatiality of Cell Behavior Ontology (CBO) models using the Visualization Tool Kit (VTK) legacy 3D model-description file
Conflict of Interest: none declared. This initial release of the CBO provides a framework for describing the objects, processes and object-to-processes links typical of multicell experiments, models and simulations
Summary
All biological research requires the use of abstract models, currently no standard method exists for describing the biological content of microscope images of tissues, in vitro experiments or in silico simulations of the tissue dynamics of multicellular systems. Representing the computational implementations (simulations) of mathematical multicell models and depend on the specific computational methodologies the modeling tools use to implement objects and their dynamic processes. As a result, these languages do not adequately document the biology that the computational model seeks to describe, i.e. you cannot recreate the biological model from the simulation code. This ad hoc approach to biological model description and distribution has several drawbacks. -change to hypoxic -change to necroƟc Hypoxic -proliferate -consume oxygen -change to normal -change to necroƟc -secrete long-diffusing proangiogenic field V(i) NecroƟc -shrink -disappear Vascular -consume oxygen field -supply oxygen field at parƟal pressure P -secrete short-diffusing chemoaƩractant field C(i) -chemotax up gradients of C(i) -elasƟcally connect to vascular and neovascular cells
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