PT  - JOURNAL ARTICLE
AU  - Patryk Burek
AU  - Nico Scherf
AU  - Heinrich Herre
TI  - On the Ontological Foundations of Cellular Development
AID  - 10.1101/2020.05.30.124875
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.05.30.124875
4099  - http://biorxiv.org/content/early/2020/05/31/2020.05.30.124875.short
4100  - http://biorxiv.org/content/early/2020/05/31/2020.05.30.124875.full
AB  - Time-lapse microscopy is a principal tool to unravel the mystery of how cells form and maintain organisms. The complexity of the domain of cellular dynamics demands a conceptual architecture as a solid theoretical foundation that supports the integration of knowledge obtained across experiments and theories. In this work, we outline the ontological foundation of cellular genealogies, a key concept for describing and representing of cellular development. We build the conceptual framework following the onto-axiomatic method: We first analyse the domain within the context of a top-level ontology (GFO). The resulting domain-specification provides the basis for a conceptualisation where we introduce concepts and relations. From these conceptualisations, we then construct model-structures adhering to the principles of model-theory. We finally elaborate axioms based on these model-structures. The developed framework provides the fundamental concepts underlying a Cell Tracking Ontology (CTO) that supports extraction and integration of biological knowledge from systems-level experiments across different types of observations at the single-cell level.Competing Interest StatementThe authors have declared no competing interest.