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  A pattern-based approach to a cell tracking ontology

Burek, P., Scherf, N., & Herre, H. (2019). A pattern-based approach to a cell tracking ontology. Procedia Computer Science, 159, 784-793. doi:10.1016/j.procs.2019.09.237.

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 Creators:
Burek, Patryk1, Author
Scherf, Nico2, 3, Author              
Herre, Heinrich4, Author
Affiliations:
1Institute of Computer Science, Faculty of Mathematics, Physics and Computer Science, Marii Curie-Sklodowskiej University, Lublin, Poland, ou_persistent22              
2Department Neurophysics (Weiskopf), MPI for Human Cognitive and Brain Sciences, Max Planck Society, ou_2205649              
3Institute for Medical Informatics and Biometry, University Hospital Carl Gustav Carus, Dresden, Germany, ou_persistent22              
4Institute for Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig, Germany, ou_persistent22              

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Free keywords: Semantic-based systems; Knowledge representation; Management; Semantic annotation of images; Videos; Ontologies
 Abstract: Time-lapse microscopy has thoroughly transformed our understanding of biological motion and developmental dynamics from single cells to entire organisms. The increasing amount of cell tracking data demands the creation of tools to make extracted data searchable and interoperable between experiment and data types. In order to address that problem, the current paper reports on the progress in building the Cell Tracking Ontology (CTO): An ontology framework for describing, querying and integrating data from complementary experimental techniques in the domain of cell tracking experiments. CTO is based on a basic knowledge structure: the cellular genealogy serving as a backbone model to integrate specific biological ontologies into tracking data. As a first step we integrate the Phenotype and Trait Ontology (PATO) as one of the most relevant ontologies to annotate cell tracking experiments. The CTO requires both the integration of data on various levels of generality as well as the proper structuring of collected information. Therefore, in order to provide a sound foundation of the ontology, we have built on the rich body of work on top-level ontologies and established three generic ontology design patterns addressing three modeling challenges for properly representing cellular genealogies, i.e. representing entities existing in time, undergoing changes over time and their organization into more complex structures such as situations.

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Language(s): eng - English
 Dates: 2019-10-142019
 Publication Status: Published in print
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 Identifiers: DOI: 10.1016/j.procs.2019.09.237
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Title: Procedia Computer Science
Source Genre: Journal
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Publ. Info: Amsterdam : Elsevier B.V.
Pages: - Volume / Issue: 159 Sequence Number: - Start / End Page: 784 - 793 Identifier: ISSN: 1877-0509
CoNE: https://pure.mpg.de/cone/journals/resource/1877-0509