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Ontology for Cellular Senescence Mechanisms

Yamagata, Y.; Fukuyama, T.; Onami, S.; Masuya, H.

2023-03-10 cell biology
10.1101/2023.03.09.531883 bioRxiv
Show abstract

Although cellular senescence is a key factor in organismal aging, with both positive and negative effects on individuals, its mechanisms remain largely unknown. Thus, integrating knowledge is essential to explain how cellular senescence manifests in tissue damage and age-related diseases. Here, we propose an ontological model that organizes knowledge of cellular senescence in a computer-readable form. We manually annotated and defined cellular senescence processes, molecules, anatomical structures, phenotypes, and other entities based on the Homeostasis Imbalance Process ontology. We described the mechanisms as causal relationships of processes and modeled a homeostatic imbalance between stress and stress response in cellular senescence for a unified framework. HoIP was assessed formally, and the relationships between cellular senescence and disease were inferred for higher-order knowledge processing. We visualized cellular senescence processes to support knowledge utilization. Our study provides a knowledge base to help elucidate mechanisms linking cellular and organismal aging.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.