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.

中文翻译：

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论细胞发育的本体论基础

延时显微镜是揭开细胞如何形成和维持生物体之谜的主要工具。细胞动力学领域的复杂性要求概念架构作为坚实的理论基础，支持跨实验和理论获得的知识的整合。在这项工作中，我们概述了细胞谱系的本体论基础，这是描述和代表细胞发育的关键概念。我们按照本体论方法构建概念框架：我们首先在顶级本体（GFO）的上下文中分析域。由此产生的领域规范为我们引入概念和关系的概念化提供了基础。从这些概念上，我们接着构建遵循模型理论原理的模型结构。最后，我们基于这些模型结构详细阐述了公理。所开发的框架提供了细胞跟踪本体论（CTO）的基本概念，该概念支持从系统级实验中跨单细胞级别的不同类型观察值提取和整合生物学知识。