메뉴 건너뛰기




Volumn 6, Issue 12, 2011, Pages

Physical properties of biological entities: An introduction to the ontology of physics for biology

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOPHYSICS; ELECTRIC POTENTIAL; MATHEMATICAL COMPUTING; ONTOLOGY OF PHYSICS FOR BIOLOGY; PHYSICAL PHENOMENA; REFERENCE DATABASE; SYSTEMS BIOLOGY; THERMODYNAMICS; BIOLOGY; PHYSICS;

EID: 84455173245     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0028708     Document Type: Article
Times cited : (34)

References (66)
  • 1
    • 35649001607 scopus 로고
    • A quantitative description of membrane current and its application to conduction and excitation in nerve
    • Hodgkin AL, Huxley AF, (1952) A quantitative description of membrane current and its application to conduction and excitation in nerve. J Physiol 117: 500-544.
    • (1952) J Physiol , vol.117 , pp. 500-544
    • Hodgkin, A.L.1    Huxley, A.F.2
  • 3
    • 2442598065 scopus 로고    scopus 로고
    • The IUPS Physiome Project: a framework for computational physiology
    • Hunter PJ, (2004) The IUPS Physiome Project: a framework for computational physiology. Prog Biophys Mol Biol 85: 551-569.
    • (2004) Prog Biophys Mol Biol , vol.85 , pp. 551-569
    • Hunter, P.J.1
  • 5
    • 0037288767 scopus 로고    scopus 로고
    • Systems biology: integrating technology, biology, and computation
    • Hood L, (2003) Systems biology: integrating technology, biology, and computation. Mech Ageing Dev 124: 9-16.
    • (2003) Mech Ageing Dev , vol.124 , pp. 9-16
    • Hood, L.1
  • 8
    • 77952898461 scopus 로고    scopus 로고
    • Ontologies in Quantitative Biology: A Basis for Comparison, Integration, and Discovery
    • Jensen LJ, Bork P, (2010) Ontologies in Quantitative Biology: A Basis for Comparison, Integration, and Discovery. PLoS Biol 8: e1000374.
    • (2010) PLoS Biol , vol.8
    • Jensen, L.J.1    Bork, P.2
  • 9
    • 33846914328 scopus 로고    scopus 로고
    • The practical impact of ontologies on biomedical informatics
    • Cimino JJ, Zhu X, (2006) The practical impact of ontologies on biomedical informatics. Yearb Med Inform pp. 124-135.
    • (2006) Yearb Med Inform , pp. 124-135
    • Cimino, J.J.1    Zhu, X.2
  • 10
    • 77958567473 scopus 로고    scopus 로고
    • Available: via the Internet. Accessed 2010
    • The Open Biological and Biomedical Ontologies (2010) Available: http://obofoundry.org/ via the Internet. Accessed 2010.
    • (2010) The Open Biological and Biomedical Ontologies
  • 11
    • 67849128700 scopus 로고    scopus 로고
    • BioPortal: ontologies and integrated data resources at the click of a mouse
    • Noy NF, Shah NH, Whetzel PL, Dai B, Dorf M, et al. (2009) BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res 37: W170-173.
    • (2009) Nucleic Acids Res , vol.37
    • Noy, N.F.1    Shah, N.H.2    Whetzel, P.L.3    Dai, B.4    Dorf, M.5
  • 13
    • 14044275403 scopus 로고    scopus 로고
    • Anatomical ontologies: names and places in biology
    • Baldock R, Burger A, (2005) Anatomical ontologies: names and places in biology. Genome Biol 6: 108.
    • (2005) Genome Biol , vol.6 , pp. 108
    • Baldock, R.1    Burger, A.2
  • 14
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
    • (2000) Nat Genet , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3    Botstein, D.4    Butler, H.5
  • 15
    • 75849153303 scopus 로고    scopus 로고
    • The Universal Protein Resource (UniProt) in 2010
    • UniProt C
    • UniProt C (2010) The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Research 38: D142-D148.
    • (2010) Nucleic Acids Research , vol.38
  • 19
    • 84855548128 scopus 로고    scopus 로고
    • Available: via the Internet. Accessed 2011
    • Ontology for Biomedical Investigations (2010) Available: http://purl.obolibrary.org/obo/obi via the Internet. Accessed 2011.
    • (2010) Ontology for Biomedical Investigations
  • 20
    • 84855531599 scopus 로고    scopus 로고
    • IUPAC Gold Book Glossary of Quantities, Available: via the Internet. Accessed 2011
    • IUPAC Gold Book Glossary of Quantities (2006) Available: http://goldbook.iupac.org/list_goldbook_quantities_defs_A.html via the Internet. Accessed 2011.
    • (2006)
  • 21
    • 33645795196 scopus 로고    scopus 로고
    • Integrating Evolution and Development: The Need for Bioinformatics in Evo-Devo
    • Mabee PM, (2006) Integrating Evolution and Development: The Need for Bioinformatics in Evo-Devo. Bio Science 56: 301-309.
    • (2006) Bio Science , vol.56 , pp. 301-309
    • Mabee, P.M.1
  • 22
    • 84855546483 scopus 로고    scopus 로고
    • PATO - Phenotypic Quality Ontology, Available: via the Internet. Accessed 2011
    • PATO- Phenotypic Quality Ontology (2010) Available: http://obofoundry.org/wiki/index.php/PATO:Main_Page via the Internet. Accessed 2011.
    • (2010)
  • 23
    • 26844450908 scopus 로고    scopus 로고
    • The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information
    • Smith CL, Goldsmith CA, Eppig JT, (2005) The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biol 6: R7.
    • (2005) Genome Biol , vol.6
    • Smith, C.L.1    Goldsmith, C.A.2    Eppig, J.T.3
  • 24
    • 33947680868 scopus 로고    scopus 로고
    • Model storage, exchange and integration
    • Le Novere N, (2006) Model storage, exchange and integration. BMC Neuroscience 7: S11.
    • (2006) BMC Neuroscience , vol.7
    • Le Novere, N.1
  • 25
    • 77958605844 scopus 로고    scopus 로고
    • Adding a little reality to building ontologies for biology
    • Lord P, Stevens R, (2010) Adding a little reality to building ontologies for biology. PLoS One 5: e12258.
    • (2010) PLoS One , vol.5
    • Lord, P.1    Stevens, R.2
  • 26
    • 11144314658 scopus 로고    scopus 로고
    • Linking ontologies with three-dimensional models of anatomy to predict the effects of penetrating injuries
    • Rubin D, Bashir Y, Grossman D, Dev P, Musen M, (2004) Linking ontologies with three-dimensional models of anatomy to predict the effects of penetrating injuries. Conf Proc IEEE Eng Med Biol Soc 5: 3128-3131.
    • (2004) Conf Proc IEEE Eng Med Biol Soc , vol.5 , pp. 3128-3131
    • Rubin, D.1    Bashir, Y.2    Grossman, D.3    Dev, P.4    Musen, M.5
  • 27
    • 38449089399 scopus 로고    scopus 로고
    • Chalkboard: Ontology-Based Pathway Modeling And Qualitative Inference Of Disease Mechanisms
    • Cook DL, Gennari JH, Wiley JC, (2007) Chalkboard: Ontology-Based Pathway Modeling And Qualitative Inference Of Disease Mechanisms. Pac Symp Biocomput 12: 16-27.
    • (2007) Pac Symp Biocomput , vol.12 , pp. 16-27
    • Cook, D.L.1    Gennari, J.H.2    Wiley, J.C.3
  • 28
    • 40549119235 scopus 로고    scopus 로고
    • Integration of multi-scale biosimulation models via light-weight semantics
    • Gennari JH, Neal ML, Carlson BE, Cook DL, (2008) Integration of multi-scale biosimulation models via light-weight semantics. Pac Symp Biocomput pp. 414-425.
    • (2008) Pac Symp Biocomput , pp. 414-425
    • Gennari, J.H.1    Neal, M.L.2    Carlson, B.E.3    Cook, D.L.4
  • 30
    • 0003066845 scopus 로고
    • An Ontology for Engineering Mathematics
    • In: Doyle J, Torasso P, Sandewall E, editors, Bonn, Germany, Morgan Kaufmann
    • Gruber TR, Olsen GR, (1994) An Ontology for Engineering Mathematics. In: Doyle J, Torasso P, Sandewall E, editors. Gustav Stressman Institut Bonn, Germany Morgan Kaufmann.
    • (1994) Gustav Stressman Institut
    • Gruber, T.R.1    Olsen, G.R.2
  • 31
    • 22944483921 scopus 로고
    • Remarks on the Mathematical Classification of Physical Quantities
    • Maxwell JC, (1871) Remarks on the Mathematical Classification of Physical Quantities. Proceedings of the London Mathematical Society 2: 224-232.
    • (1871) Proceedings of the London Mathematical Society , vol.2 , pp. 224-232
    • Maxwell, J.C.1
  • 33
    • 0015581672 scopus 로고
    • Network thermodynamics: dynamic modelling of biophysical systems
    • Oster GF, Perelson AS, Katchalsky A, (1973) Network thermodynamics: dynamic modelling of biophysical systems. Q Rev Biophys 6: 1-134.
    • (1973) Q Rev Biophys , vol.6 , pp. 1-134
    • Oster, G.F.1    Perelson, A.S.2    Katchalsky, A.3
  • 35
    • 0034742451 scopus 로고    scopus 로고
    • Network thermodynamics and complexity: a transition to relational systems theory
    • Mikulecky DC, (2001) Network thermodynamics and complexity: a transition to relational systems theory. Comput Chem 25: 369-391.
    • (2001) Comput Chem , vol.25 , pp. 369-391
    • Mikulecky, D.C.1
  • 41
    • 11144278588 scopus 로고    scopus 로고
    • Computational Cardiology
    • In: Goos G, Hartmanis J, van Leeuwen J, editors, Berlin, Heidelberg, Germany, Springer-Verlag
    • Sachse FB, (2004) Computational Cardiology. In: Goos G, Hartmanis J, van Leeuwen J, editors. Modeling of Anatomy, Electrophysiology, and Mechanics Berlin, Heidelberg, Germany Springer-Verlag.
    • (2004) Modeling of Anatomy, Electrophysiology, and Mechanics
    • Sachse, F.B.1
  • 44
    • 0037315604 scopus 로고    scopus 로고
    • Stoichiometric network theory for nonequilibrium biochemical systems
    • Qian H, Beard DA, Liang SD, (2003) Stoichiometric network theory for nonequilibrium biochemical systems. Eur J Biochem 270: 415-421.
    • (2003) Eur J Biochem , vol.270 , pp. 415-421
    • Qian, H.1    Beard, D.A.2    Liang, S.D.3
  • 45
    • 18944374341 scopus 로고    scopus 로고
    • Biodynamic ontology: applying BFO in the biomedical domain
    • In: Pisanelli DM, editors, Amsterdam, IOS Press
    • Grenon P, Smith B, Goldberg L, (2004) Biodynamic ontology: applying BFO in the biomedical domain. In: Pisanelli DM, editors. Ontologies in Medicine Amsterdam IOS Press pp. 20-38.
    • (2004) Ontologies in Medicine , pp. 20-38
    • Grenon, P.1    Smith, B.2    Goldberg, L.3
  • 47
    • 84855546486 scopus 로고    scopus 로고
    • WonderWeb Deliverable D18. The WonderWeb Library of Foundational Ontologies and the DOLCE ontology, Available: via the Internet. Accessed 2010
    • WonderWeb Deliverable D18. The WonderWeb Library of Foundational Ontologies and the DOLCE ontology (2003) Available: http://wonderweb.semanticweb.org/deliverables/documents/D18.pdf via the Internet. Accessed 2010.
    • (2003)
  • 48
    • 84855545258 scopus 로고    scopus 로고
    • OWL Working Group, Available: via the Internet. Accessed 2010
    • OWL Working Group (2011) Available: http://www.w3.org/2007/OWL/wiki/OWL_Working_Group via the Internet. Accessed 2010.
    • (2011)
  • 49
    • 84855546482 scopus 로고    scopus 로고
    • NCBO BioPortal, Available: via the Internet. Accessed 2010
    • NCBO BioPortal (2010) Available: http://bioportal.bioontology.org/ via the Internet. Accessed 2010.
    • (2010)
  • 51
    • 51649208695 scopus 로고
    • Dimensional Analysis In Mathematical Biology
    • Stahl WR, (1961) Dimensional Analysis In Mathematical Biology. Bulletin of Mathematical Biophysics 23: 355.
    • (1961) Bulletin of Mathematical Biophysics , vol.23 , pp. 355
    • Stahl, W.R.1
  • 52
    • 84855550645 scopus 로고    scopus 로고
    • The Unified Code for Units of Measure, Available: via the Internet. Accessed 2010
    • The Unified Code for Units of Measure (2005) Available: http://aurora.regenstrief.org/UCUM/ucum.html via the Internet. Accessed 2010.
    • (2005)
  • 53
    • 0001740359 scopus 로고
    • Die Grundform des arterielen Pulses erste Abhandlung: mathematische Analyse
    • Frank O, (1899) Die Grundform des arterielen Pulses erste Abhandlung: mathematische Analyse. Z Biol 37: 483-526.
    • (1899) Z Biol , vol.37 , pp. 483-526
    • Frank, O.1
  • 55
    • 0030285463 scopus 로고    scopus 로고
    • Mereotopology: A theory of parts and boundaries
    • Smith B, (1996) Mereotopology: A theory of parts and boundaries. Data & Knowledge Engineering 20: 287-303.
    • (1996) Data & Knowledge Engineering , vol.20 , pp. 287-303
    • Smith, B.1
  • 57
    • 61949441759 scopus 로고    scopus 로고
    • Advances in semantic representation for multiscale biosimulation: a case study in merging models
    • Neal ML, Gennari JH, Arts T, Cook DL, (2009) Advances in semantic representation for multiscale biosimulation: a case study in merging models. Pac Symp Biocomput pp. 304-315.
    • (2009) Pac Symp Biocomput , pp. 304-315
    • Neal, M.L.1    Gennari, J.H.2    Arts, T.3    Cook, D.L.4
  • 58
    • 73949106573 scopus 로고    scopus 로고
    • Bridging biological ontologies and biosimulation: the Ontology of Physics for Biology
    • Cook DL, Mejino JL, Neal ML, Gennari JH, (2008) Bridging biological ontologies and biosimulation: the Ontology of Physics for Biology. AMIA Annu Symp Proc pp. 136-140.
    • (2008) AMIA Annu Symp Proc , pp. 136-140
    • Cook, D.L.1    Mejino, J.L.2    Neal, M.L.3    Gennari, J.H.4
  • 59
    • 79952012805 scopus 로고    scopus 로고
    • Multiple ontologies in action: Composite annotations for biosimulation models
    • Gennari JH, Neal ML, Galdzicki M, Cook DL, (2011) Multiple ontologies in action: Composite annotations for biosimulation models. J Biomed Inform 44: 146-154.
    • (2011) J Biomed Inform , vol.44 , pp. 146-154
    • Gennari, J.H.1    Neal, M.L.2    Galdzicki, M.3    Cook, D.L.4
  • 61
    • 85044709226 scopus 로고    scopus 로고
    • Composite Annotations: Requirements for Mapping Multiscale Data and Models to Biomedical Ontologies; Minneapolis, MN
    • Cook DL, Mejino JLV, Neal ML, Gennari JH, (2009) Composite Annotations: Requirements for Mapping Multiscale Data and Models to Biomedical Ontologies; Minneapolis, MN. IEEE.
    • (2009) IEEE
    • Cook, D.L.1    Mejino, J.L.V.2    Neal, M.L.3    Gennari, J.H.4
  • 63
    • 84855546480 scopus 로고    scopus 로고
    • Systems Biology Ontology, Available: via the Internet. Accessed 2011
    • Systems Biology Ontology (2006) Available: http://www.ebi.ac.uk/sbo/ via the Internet. Accessed 2011.
    • (2006)
  • 64
    • 84855545251 scopus 로고    scopus 로고
    • Biomodels Database - A Database of Annotated Published Models, Available: via the Internet. Accessed 2011
    • Biomodels Database- A Database of Annotated Published Models (2011) Available: http://www.ebi.ac.uk/biomodels-main/ via the Internet. Accessed 2011.
    • (2011)
  • 65
    • 84855545252 scopus 로고    scopus 로고
    • NSR Physiome Model Wiki, Available: via the Internet. Accessed 2011
    • NSR Physiome Model Wiki (2007) Available: http://www.physiome.org/Models/ via the Internet. Accessed 2011.
    • (2007)
  • 66
    • 77951012337 scopus 로고    scopus 로고
    • Foundational Process Relations in Bio-Ontologies
    • In: Galton A, Mizoguchi R, editors, IOS Press
    • Ozgovde A, Gruninger M, (2010) Foundational Process Relations in Bio-Ontologies. In: Galton A, Mizoguchi R, editors. Formal Ontology in Information Systems IOS Press.
    • (2010) Formal Ontology in Information Systems
    • Ozgovde, A.1    Gruninger, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.