The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents

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.

BioCAE: A New Strategy of Complex Biological Systems for Biofabrication of Tissues and Organs

“…These diverse levels coupling intra and interscale interactions make a biological system extremely complex, requiring advanced mathematical and computational models for the integration of the different scales [15,16]. There is a range of multi-scale modelling methods that could potentially be employed in systems biology [17][18][19][20][21][22] and consequently in the biofabrication of tissues and organs. Then, in the next section, we will describe some multi-scale approaches and/or software which may be part of the BioCAE and that are playing or will play important roles in multi-scale problems in systems biology and tissues biofabricated, thereby preventing a large amount of trial and error experiments in laboratories.…”

“…Modelling and simulation of diffusion process in tissue spheroids CFD [14] Agent-based virtual tissue simulations CC3D [17] Cell compressibility, motility and contact inhibition on the growth of tumor cell clusters CC3D [18] Multiscale modeling of the early CD8 T cell immune response in lymph nodes CC3D [19] Multi-scale knowledge on cardiac development CC3D [20] The cell behavior ontology CC3D [21] Cell differentiation in the transition to multicellularity CC3D [22] Dynamics of cell aggregates fusion CC3D [36] A multi-cell model of tumor evolution CC3D [37] Virtual tissues MAS [38] Disruption of blood vessel development CC3D [39] Tumor growth and angiogenesis CC3D [40] Agent-oriented in silico liver (ILS) MAS [41] Model of thrombus development MAS (TS) [42] Three-dimensional multi-scale tumor model MAS [43] A multi-scale model of dendritic cell education and trafficking in the lung CM [44] Multi-scale model of follicular development CM [45] Multi-scale in silico leukocytes model MAS [46] Multi-scale model of organogenesis CM [47] Limitations of spheroids under inappropriate conditions FE [48] Finite lower levels occur at multiple time scales influencing the behavior of the organ. Multi-scale models are usually based on the continuum modeling and/or MAS approaches which can be decomposed into N single-scale mathematical models and several physical processes.…”

“…Multi-scale models are usually based on the continuum modeling and/or MAS approaches which can be decomposed into N single-scale mathematical models and several physical processes. Various works have already been done which apply many multi-scale methods in several biological systems [14,[17][18][19][20][21][22][36][37][38][39][40][41][42][43][44][45][46][47][48][49]: a good review is proposed in Table 1.…”

MultiCellDS: a standard and a community for sharing multicellular data

“…We must next characterize cell networks, including cell-cell interactions, cell mutations, and cell lineages. These enhancements can be woven into MultiCellDS using complementary ontologies, such as the Cell Behavior Ontology [13].…”

“…We must next characterize cell networks, including cell-cell interactions, cell mutations, and cell lineages. These enhancements can be woven into MultiCellDS using complementary ontologies, such as the Cell Behavior Ontology [13].We must also expand the phenotype datasets to incorporate other critical measurements, such as genomic, proteomic, and metabolomics data. Moreover, we must account for the hysteresis in cell phenotype parameters: cells undergoing stresses do not always return to their original phenotypes once the stresses are removed.…”