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Physical Properties of Biological Entities: An Introduction to the Ontology of Physics for Biology
- Source :
- PLoS ONE, Vol 6, Iss 12, p e28708 (2011), PLoS ONE
- Publication Year :
- 2011
- Publisher :
- Public Library of Science (PLoS), 2011.
-
Abstract
- As biomedical investigators strive to integrate data and analyses across spatiotemporal scales and biomedical domains, they have recognized the benefits of formalizing languages and terminologies via computational ontologies. Although ontologies for biological entities—molecules, cells, organs—are well-established, there are no principled ontologies of physical properties—energies, volumes, flow rates—of those entities. In this paper, we introduce the Ontology of Physics for Biology (OPB), a reference ontology of classical physics designed for annotating biophysical content of growing repositories of biomedical datasets and analytical models. The OPB's semantic framework, traceable to James Clerk Maxwell, encompasses modern theories of system dynamics and thermodynamics, and is implemented as a computational ontology that references available upper ontologies. In this paper we focus on the OPB classes that are designed for annotating physical properties encoded in biomedical datasets and computational models, and we discuss how the OPB framework will facilitate biomedical knowledge integration.
- Subjects :
- Biomedical knowledge
Biophysics
lcsh:Medicine
Bioengineering
Biology
Ontology (information science)
Bioinformatics
Biophysics Simulations
Classical physics
Biophysics Theory
Open Biomedical Ontologies
03 medical and health sciences
0302 clinical medicine
Ontology and Logics
Biological Systems Engineering
Biochemical Simulations
Upper ontology
lcsh:Science
030304 developmental biology
Physics
0303 health sciences
Computational model
Multidisciplinary
Extramural
Chemistry
Systems Biology
Bio-Ontologies
lcsh:R
Computational Biology
Semantic framework
Data science
Computer Science
Thermodynamics
Biophysic Al Simulations
lcsh:Q
030217 neurology & neurosurgery
Research Article
Biotechnology
Subjects
Details
- ISSN :
- 19326203
- Volume :
- 6
- Database :
- OpenAIRE
- Journal :
- PLoS ONE
- Accession number :
- edsair.doi.dedup.....857675b2abd67e86bc8e9bc85438d2ee