Ontology of Physics for Biology

Last uploaded: July 19, 2019
Preferred Name

Physics entity

Definitions

A Thing that is a quality, definition, abstraction, or law of classical physics as discovered and applied to the explanation, analysis, and simulation of biophysical entities and processes.

ID

http://bhi.washington.edu/OPB#OPB_00528

comment

A Thing that is a quality, definition, abstraction, or law of classical physics as discovered and applied to the explanation, analysis, and simulation of biophysical entities and processes.

discussion

The OPB is an ontology of the real entities and their abstractions modeled using the science of classical physics for the description and analyisis of physical entities such as an apple or rope, or for systems of interacting entities. It includes branches of engineering system dynamics and classical thermodynamics. OPB has been formulated to support the development, annotation, description and sharing of analytical models. Although developed in the domain of biology, biophysics and physiology, its underlying assumptions, form and content is applicable for the analysis of non-biological engineering systems. OPB aims to facilitate and expedite the annotation and cross-referencing of physics-based analytical models in the broad realm of biomedicine. In curating the OPB, we have strived to represent biophysical knowledge of applicable to biological physical entities, processes, and functions using the formal tools and concepts of computational ontology as expressed in description logic (DL),and web ontology language (OWL). OPB has classes that represent abstractions of key classes in BFO such as BFO:Continuant (OPB:Physics continuant). BFO:Processural entity (OPB:Processural entity), and BFO:Attribute (OPB:Physics attribute). A key differentiator is that OPB represents physical entities not represented in BFO such thermodynamic energy, potential energy fields, information. In particular, OPB:Physical process ia defined as the flow of energy and/or information amongst process participants. These are essential concepts for explaining, understanding and testing of biophysical hypotheses. To emphasize intent of the OPB as an ontology of analytical concepts, we have purposely named its top class and its subclasses using the term "Physics" to reference the science of physics rather than the term "physical" which could imply that OPB intends to represent the "real" physical world. The OPB does not extend to include quantum or relativistic physics, nor is it intended to recapitulate the axiomatic basis of physics as a theoretical framework. Rather, OPB is focuses on foundational theory of classical physics particularly as applied in system dynamics. For example, it encompasses discrete systems analysis (using ordinary differential equations; ODEs), continuum systems analysis (using partial differential equations; PDEs), discrete "agent-based" modeling, and causal propagation models. the first version of the OPB is targeted solely to discrete systems analysis.

label

Physics entity

prefixIRI

OPB:OPB_00528

prefLabel

Physics entity

subClassOf

http://www.w3.org/2002/07/owl#Thing

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