OPB-Based Semantic Modeling
Daniel L. Cook, John H. Gennari, Maxwell Lewis Neal · 2023
A primary aim in developing the Ontology of Physics for Biology (OPB) was to create a logical, computable framework for organizing mechanistic biological knowledge across physical scales and biological research domains. This chapter discusses several applications of the OPB that illustrate its utility and that highlight the use-cases that have driven its development. Given the multitude of modeling formats used by modelers, semantic annotations provide a valuable common ground for capturing the biological meaning of what models simulate. Composite annotations are built using knowledge resource terms from ontologies where terms are linked to each other via class hierarchies, partonomies, and other topologies. The SemSim architecture was designed to represent the computational and biological aspects of simulation models across a wide variety of research domains and simulation formats. Constructing a semantically-integrated physiome would also give researchers the power to explore mechanistic connections between physiological features of interest.