Ontologies
From CBO
Development of a Cell Behavior Ontology
Ontologies are logical structures which provide formal descriptions of (scientific) concepts, hierarchies of terms with agreed meanings and relationships. Some examples of ontology-related projects for biology include the Gene Ontology, MGED, SBO and KiSAO. When successful (as with the Gene Ontology which is a major component of the Genomic revolution), they enable seamless integration of software and unambiguous specification of meaning. However, despite these large projects and some specific and valuable earlier efforts, we do not yet have agreed-upon definitions of the meaning of such apparently simple cell behaviors as cell division, cell polarization or cell movement. Such a structure is crucial to modern scientific communication and for coherent development of software applications relating to multicellular organization (e.g. cancer biology, developmental biology, regenerative medicine, plant biology and certain aspects of microbiology). Ontologies are tools to help create taxonomies; the CBO will create a framework for discussion of cell behaviors and provide structure that will eventually permit implementation-independent model definitions and transparent communication between simulations developed by different modeling groups and addressing different modeling scales. Our focus is not to duplicate existing efforts, but to identify and fill a gap left by existing ontologies, which describe subcellular behaviors and static tissue-level properties, but mostly neglect the dynamic behavioral life of cells.
Generating a viable ontology requires expertise in a range of fields, experimental biology to define cell behaviors and their scope and modifiers, mathematical biology and biosimulation to define needed conceptual structures, and ontology development to ensure that the structures are logically consistent and that our work-flow is as efficient as possible. We aim to have roughly equal representation of these areas among our 20-25 participants.
Our goal for this workshop is to complete a top-level draft ontology describing cell behaviors which is acceptable to the broad bioscience community. This initial draft will, after a comment period, form the basis for the ongoing development of the CBO and a joint publication of the initial standard. Because we are tightly focused on this goal, our workshop schedule includes a minimal number of overview talks to orient participants on the first half day, followed by two and a half days of intensive consultation as a group and in breakouts addressing specific areas of behavior (e.g. cell motility or cell division).
