Construction of a Cell Death Ontology based on a Device Ontology that Allows Include Unknown Factors -Description of molecule behaviors and systems based on hierarchical classification of Functions-

Abstract

Computational simulations are expected to play an important role in understanding of unspecified factors in biological phenomena. To implement computational simulations in biology, therefore, construction, knowledge in biological phenomena is accumulated as qualitative descriptions in natural languages on literature. Construction of ontologies is adapted to translate such literature knowledge into knowledge representation available for computers. Simulations are indispensable in revealing new factors in a phenomenon which haven 't been empirically observed yet. Ontologies focusing on functions enable such simulations to verify new factors assumed to be. In this study, we classified functions hierarchically to build an ontology for a signal transduction of programmed cell death. We then constructed an ontology about molecule behaviors and systems in apoptosis, which is one type of programmed cell deaths, based on these hierarchical functions. We also discussed a method to identify unknown molecules by comparing their structures.