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Foundations of the Cell Tracking Ontology

Time-lapse microscopy gives us insight into the dynamic behaviour of cells as they develop into tissues, organs, and entire organisms. Being able to image and analyse these multi-cellular dynamics might provide the key to understand the underlying organising principles. There is an ever increasing amount of available cell tracking data that could be systematically integrated to increase our knowledge of the organizing biological processes. This integration of heterogeneous data demands the creation of frameworks suitable for rendering extracted data searchable and interoperable between experiments and even data from complementary measurements such as single cell sequencing. In the current paper we discuss the fundamental concept of a cellular genealogy, a basic knowledge structure forming conceptual and formal foundations of the Cell Tracking Ontology (CTO) suitable for describing, querying and integrating data from complementary experimental techniques in the domain of single cell analysis. Cellular genealogies allow integration of cell tracking data, which typically consist of sets of observations of cells at single time points organized into time indexed sequences mapping the behaviour (e.g. cell division, cell death or differentiation) of individual cells and their offspring into a common reference frame. The current paper discusses the main ontological components of cellular genealogies: cells, considered as material objects, having a lifetime and persisting through time; temporal situations, composed of (continual) cells and relators connecting these cells; snapshots of cells and of temporal situations; frames identified with snapshots of temporal situations (they may be called presentic situations). All these entities are organized into cellular genealogies, forming consistent, pedigreelike structures supporting organization, querying and analysis of cell tracking data.