AbstractTime-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.
%0 Unpublished Work
%1 Burek2020-av
%A Burek, Patryk
%A Scherf, Nico
%A Herre, Heinrich
%D 2020
%J bioRxiv
%K
%T On the ontological foundations of cellular development
%X AbstractTime-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.
@unpublished{Burek2020-av,
abstract = {AbstractTime-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.},
added-at = {2024-09-10T11:56:37.000+0200},
author = {Burek, Patryk and Scherf, Nico and Herre, Heinrich},
biburl = {https://puma.scadsai.uni-leipzig.de/bibtex/2be23a12a2987f422108f4bf8060a4363/scadsfct},
institution = {bioRxiv},
interhash = {3bf8769a7219e3199372d007481ba0d5},
intrahash = {be23a12a2987f422108f4bf8060a4363},
journal = {bioRxiv},
keywords = {},
month = may,
timestamp = {2024-09-10T15:15:57.000+0200},
title = {On the ontological foundations of cellular development},
year = 2020
}
