Composição de modelos para a fisiologia: uma proposta de infraestrutura de e-science baseada em ontologias
Resumo
A quantidade e variedade de informações geradas pelas ciências biológicas têm levado a um uso intenso de modelos na área. Neste contexto, tanto a modelagem matemática quanto a modelagem computacional necessitam de uma descrição acurada que permita que esses modelos sejam compartilhados e simulados como foram formulados por seus criadores. CellML é uma linguagem de marcação que permite a descrição de variáveis, equações e componentes de modelos biológicos, mas é insuficiente para representar a semântica de tais modelos. Nossa pesquisa busca expressar de maneira formal a semântica desses modelos, através do uso de ontologias. Neste artigo, apresentamos a Cell Component Ontology – CelO, uma ontologia expressa em OWL-DL, que captura tanto a estrutura do modelo de uma célula quanto as propriedades dos seus componentes funcionais. A ontologia CelO é utilizada em uma arquitetura orientada a serviços para descrever, realizar inferências e consultar os modelos CellML. O objetivo principal da arquitetura é facilitar o reuso e a composição dos componentes existentes e permitir a validação semântica de novos modelos.
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Nielsen P. et al. (2003) “Ontologies in CellML: A Versatile Method to Describe Cellular Models”. IIth International conference on Intelligent Systems for Molecular Biology (ISMB). International Society for Computational Biology(ISCB). (2003)
PCEnv (2008) “Physiome CellML Environment”. Disponível em: [link].
Pellet (2008) “Pellet: The Open Source OWL DL Reasoner”. Disponível em: [link].
Protégé (2008) “Protege OWL – Ontology Editor for Semantic Web”. Disponível em: [link].
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SBML (2008) “Systems Biology Markup Language”. Disponível em: [link].
Shimayoshi, T. et al. (2006) “A Method to Support Cell Physiological Modelling Using Description Language and Ontology”. IPSJ Digital Courier, 2:726-735, 2006.
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Bechhofer, S. et al. (2004) “OWL web ontology language 1.0 reference”. Disponível em: [link].
Beeler, G. W., Reuter, H. (1977) “Reconstruction of the action potential of ventricular myocardial fibres”. Journal of Physiology , 268, 177-210.
Berners-Lee, T. et al. (2001) “The Semantic Web. A new form of Web content that is meaningful to computers will unleash a revolution of new possibilities”. Scientific American.
Borst, W.N. (1997) “Construction of Engineering Ontologies”. Phd Thesis. Disponível em: [link].
CellML (2008). “Cell Markup Language”. Disponível em [link].
CellML Repository (2008) “Cell Markup Language”. Disponível em [link].
Cuellar, A. A. et al. (2006) “CellML Specification 1.1 ”. Disponível em: [link].
Finkelstein, A. et al. (2004) “Computational Challenges of Systems Biology” IEEE Computer, Vol. 37 No. 5 (2004) 26–33.
Garny A. et al. (2007) “CellML and Associated Tools and Techniques”. Paper submited to Elsevier Ireland Ltd.
Gruber, T. R. (1994) “Towards principles for the design of ontologies used for knowledge sharing”. In N. Guarino and R. Poli (Eds.), Formal Ontology in Conceptual Analysis and Knowledge Representation. Kluwer.
Halstead M. (2007) “Ontologies and Repositories ”. CellML Workshop 2007. Disponível em : [link].
Horrocks, I. et al. (2004) “SWRL: A Semantic Web Rule Language Combining OWL and RuleML”. W3C Member Submission 21 May 2004. [link].
Jess (2008) “JESS, the Rule Engine for the Java Platform”. Disponível em: [link].
Lu, J. et al. (2007) “SOR: a practical system for ontology storage, reasoning and search”. In Proceedings of the 33rd international Conference on Very Large Data Bases (Vienna, Austria, September 23 - 27, 2007). Very Large Data Bases. VLDB Endowment, 1402-1405.
Luo, C., Rudy, Y. (1991) “A Model of the Ventricular Cardiac Action Potential - Depolarisation, Repolarisation and Their Interaction”, Circulation Research , 68, 1501-1526.
Luo, C., Rudy, Y. (1994) “A Dynamic Model of the Cardiac Ventricular Action Potential - Simulations of Ionic Currents and Concentration Changes”, Circulation Research , 74, 1071-1097.
Malmivuo, J., Plonsey, R. (1995) “Bioelectromagnetism: Principles and Applications of Bioelectric and Biomagnetic Fields”. Oxford University Press, New York.
Martin, D. et al. (2004) “OWL-S: Semantic Markup for Web Services”. W3C Member Submission 22 November 2004. Disponível em: [link].
Matos, E. et al. (2007) “MathWS: Broker de Serviços Web para e-Science”. 1st Brazilian e-Science WorkShop. in conjunction with 22nd Brazilian Symposium on Data Base, João Pessoa, Brazil.
Nelson, M. E. (2005) “Electrophysiological Models” In: Databasing the Brain: From Data to Knowledge. S. Koslow and S. Subramaniam (eds.) pp. 285-301, Wiley, New York.
Nickerson D, Hunter P. (2006) “The Noble cardiac ventricular electrophysiology models in CellML”. Prog Biophys Mol Biol, Jan-Apr;90(1-3):346-59.
Nielsen P. et al. (2003) “Ontologies in CellML: A Versatile Method to Describe Cellular Models”. IIth International conference on Intelligent Systems for Molecular Biology (ISMB). International Society for Computational Biology(ISCB). (2003)
PCEnv (2008) “Physiome CellML Environment”. Disponível em: [link].
Pellet (2008) “Pellet: The Open Source OWL DL Reasoner”. Disponível em: [link].
Protégé (2008) “Protege OWL – Ontology Editor for Semantic Web”. Disponível em: [link].
Sauro, H. M. et al. (2006) “Challenges for modeling and simulation methods in systems biology”. In Proceedings of the 38th Conference on Winter Simulation (Monterey, California, December 03 - 06, 2006). L. F. Perrone, B. G. Lawson, J. Liu, and F. P. Wieland, Eds. Winter Simulation Conference. Winter Simulation Conference, 1720-1730.
SBC (2006) “Grandes Desafios de Pesquisa em Computação no Brasil: 2006 – 2016 – Relatório Final”. Disponível em: [link].
SBML (2008) “Systems Biology Markup Language”. Disponível em: [link].
Shimayoshi, T. et al. (2006) “A Method to Support Cell Physiological Modelling Using Description Language and Ontology”. IPSJ Digital Courier, 2:726-735, 2006.
SPARQL. (2008) “SPARQL Query Language for RDF”. W3C Recommendation 15 January 2008. Disponível em: [link]
Sun, Z. et al. (2007) “Using Ontology with Semantic Web Services to Support Modeling in Systems Biology”. International Workshop on Approaches and Architectures for Web Data Integration and Mining in Life Sciences (WebDIM4LS), Nancy, France.
Publicado
12/07/2008
Como Citar
MATOS, Ely Edison; CAMPOS, Fernanda; BRAGA, Regina; WEBER, Rodrigo.
Composição de modelos para a fisiologia: uma proposta de infraestrutura de e-science baseada em ontologias. In: SEMINÁRIO INTEGRADO DE SOFTWARE E HARDWARE (SEMISH), 35. , 2008, Belém/PA.
Anais [...].
Porto Alegre: Sociedade Brasileira de Computação,
2008
.
p. 46-60.
ISSN 2595-6205.
