=Paper=
{{Paper
|id=Vol-3805/ICBO-2022_paper_2131
|storemode=property
|title=Knowledge Systematization for Cellular Senescence Processes by Homeostasis Imbalance Process Ontology
|pdfUrl=https://ceur-ws.org/Vol-3805/ICBO-2022_paper_2131.pdf
|volume=Vol-3805
|authors=Yuki Yamagata,Shuichi Onami,Hiroshi Masuya
|dblpUrl=https://dblp.org/rec/conf/icbo/YamagataOM22
}}
==Knowledge Systematization for Cellular Senescence Processes by Homeostasis Imbalance Process Ontology==
https://ceur-ws.org/Vol-3805/ICBO-2022_paper_2131.pdf
Knowledge Systematization for Cellular Senescence Processes by
Homeostasis Imbalance Process Ontology
Yuki Yamagata 1, 2, Shuichi Onami 1, 2, and Hiroshi Masuya2, 3
1
RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047,
Japan, 2 RIKEN Information R&D and Strategy Headquarters, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe
650-0047, Japan, 3 RIKEN BioResource Research Center, Kouyadai 3-1-1 Tsukuba, Ibaraki 305-0074 Japan
Abstract
In the science of aging, controlling cellular senescence attracts increasing attention. This study
focuses on cellular senescence and systematizes knowledge by developing the homeostasis
imbalance process ontology (HoIP). We uniformly represent a series of processes related to
cellular senescence as an imbalance between stress and its response. Moreover, we show how
cellular senescence brings benefits and deleterious effects in the embryonic, acute, and chronic
course.
Keywords 1
cellular senescence, homeostasis imbalance process ontology, knowledge systematization
1. Introduction
3. Discussion
Cellular senescence is a crucial factor in aging.
This abstract introduces an organization of This study shows that cellular senescence
knowledge concerning the processes of cellular benefits the embryonic and acute course via the
senescence. We have developed a homeostasis homeostatic imbalance. Especially in embryos,
imbalance process ontology (HoIP) the homeostatic imbalance might lead to dynamic
(https://bioportal.bioontology.org/ontologies/HO equilibrium, i.e., homeorhesis [2]. This
IP) [1]. We report the representation of the course framework also highlights the fact that chronic
of cellular senescence in HoIP. cellular senescence has deleterious tissue effects.
HoIP will aid in understanding the fundamental
2. Methods and Results mechanisms of cellular senescence.
We manually reviewed textbooks and articles 4. Acknowledgements
using Protégé 5.5.0. This work captured the
process of cellular senescence as the outcome of This work was supported by JSPS KAKENHI
homeostasis imbalance between stress (e.g., DNA Grant Number JP22K17959 and the RIKEN Open
damage) and stress response. Referring to upper Life Science Platform Project.
ontology BFO and OBO-Foundry ontologies in
biomedicine, we created a new definition of the
course of cellular senescence in HoIP. 5. References
HoIP describes each course in terms of causal
processes. For example, in the chronic cellular
senescence course, we confirmed that sustained [1] Yamagata et al. Homeostasis Imbalance
senescence-associated secretory phenotype Process Ontology: a Study on COVID-19
(SASP) secretion could cause chronic Infectious Processes, VDOS-2021, 2021.
inflammation related to oncogenesis and type 2 [2] Waddington, C. H. (2014). The strategy of
diabetes. In contrast, transient SASP might cause the genes. Routledge.
DNA repair, tissue repair, and tissue remodeling
in the embryonic and acute courses.
ICBO 2022, September 25–28, 2022, Ann Arbor, MI, USA
EMAIL: yuki.yamagata@riken.jp (A. 1)
ORCID: 000-0002-9673-1283 (A. 1)
© 2020 Copyright for this paper by its authors. Use permitted under Creative
Commons License Attribution 4.0 International (CC BY 4.0).
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