« Back to abstracts page

Building the Cell Behavior Ontology (CBO): An Illustrated Guide

Michal Galdzicki Biomedical and Health Informatics University of Wasington

Authors

Michal Galdzicki, Daniel L. Cook, Benjamin L. Zaitlen, Herbert M. Sauro, John H. Gennari

Abstract

A rigorously defined computational structure is needed to organize the myriad of cellular behavior descriptions. The Cell Behavior Ontology (CBO) is a proposed solution to develop an unambiguous language to define the concepts and the relationships which comprise cellular behavioral processes. The ontology is intended to build useful simulation models, integrate knowledge from various sources, and aid scientific communication. To guide development of this resource we demonstrate the construction of the CBO description for an example model of cell size growth as simulated in CompuCell3D. The ontology is implemented according to the theoretical scaffold set by the Ontology of Physics for Biology (OPB). Using these organizing principles for the basis of CBO we define the components of the model which specify the biological processes, the participating entities, physical properties, and how these processes are perceived in terms of measurement. The proposed base of the CBO conforms to the description of physical aspects of biological processes, therefore it aims to offer the rigor necessary for reuse in multiple contexts. For example, we hope to: Establish the development of criteria for biological simulation model descriptions from the perspective of the biological phenomenon described; Offer the computational methodology to annotate cellular image time series data; and facilitate sharing of defined data in scientific communication. We strive towards an implementation of the computational structure of the CBO to carry the necessary semantics. The CBO, as a community standard, can provide in silico and in vivo studies with a framework to consistently annotate biological processes observed at multiple scales. We hope to advance the development of the CBO using the cell size growth example as a template to describe the many other cellular processes.