Ontology of Physics for Biology
Developed in United States
Created in 2007
Scope and data types
How to cite this record FAIRsharing.org: OPB; Ontology of Physics for Biology; DOI: https://doi.org/10.25504/FAIRsharing.qcceez; Last edited: Feb. 22, 2018, 1:58 p.m.; Last accessed: Oct 17 2018 9 p.m.
Record updated: Oct. 23, 2016, 10:47 p.m. by The FAIRsharing Team.
Edits to 'https://fairsharing.org/FAIRsharing.qcceez' by 'The FAIRsharing Team' at 22:47, 23 Oct 2016 (approved): 'description' has been modified: Before: The OPB is an ontology of the abstractions created by the sciences of classical physics and thermodynamics particularly as formulated for analytical purposes by the engineering concepts of system dynamics. Aside from its dependence on classical physics, the OPB does not purport to be a philosophically-based representation of physical "reality". Their goal is the annotation and cross-referencing of physics-based analytical models in the broad realm of biomedicine. The OPB does not include quantum or relativistic physics, nor is it intended to recapitulate the axiomatic basis of physics as a theoretical framework. Whereas the foundational theory of the OPB encompasses both discrete systems analysis (using ordinary differential equations; ODEs) and continuum systems analysis (using partial differential equations; PDEs), the first version of the OPB is targeted solely to discrete systems analysis. In curating the OPB, we have strived to represent biological and biophysical knowledge of biological function using the formal tools and concepts of computational ontology as expressed in description logic (DL), web ontology language (OWL), and "upper ontologies" such as General Formal Ontology (GFO) and Basic Formal Ontology (BFO). After: The Ontology of Physics for Biology is a reference of classical physics as applied to the dynamics of biological systems. This resource provides a reference ontology of physical properties (e.g., pressure, chemical concentration) and principles (e.g., Ohms law, Fickes law) by which the physical meaning of biosimulation models may be annotated. Publication List has changed: Previous values: Physical properties of biological entities: an introduction to the ontology of physics for biology. New values: Physical properties of biological entities: an introduction to the ontology of physics for biology. Bridging Biological Ontologies and Biosimulation: The Ontology of Physics for Biology Ontology of physics for biology: representing physical dependencies as a basis for biological processes. Organisations have changed: Previous values: Semantics of Biological Processes Group New values: Semantics of Biological Processes Group European Commission FP7 Support links have changed: Previous values: New values: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2656075/ Grants have changed: Previous values: New values: R01 HL087706-01 GM094503
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Physical properties of biological entities: an introduction to the ontology of physics for biology.
Cook DL,Bookstein FL,Gennari JH
PLoS One 2012
Bridging Biological Ontologies and Biosimulation: The Ontology of Physics for Biology
Cook DL, Mejino JLV, Neal ML, Gennari JH.
AMIA Annual Symposium Proceedings 2008
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European Commission FP7 (Government body)
US National Institute of General Medical Sciences, (NIGMS) (Government body)
US National Institutes of Health (NIH) (Research institute)
GM094503 (US National Institute of General Medical Sciences, (NIGMS))
R01 HL087706-01 (U.S. National Library of Medicine)