CelOWS: uma arquitetura orientada a serviços para definição, pesquisa e reuso de modelos biológicos
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, reutilizados e simulados tal como foram formulados por seus criadores. 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.Referências
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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.
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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: http://www.w3.org/Submission/OWL-S/.
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.
MONET (2006) MONET Consortium. MONET Home Page, www. Available from http://monet.nag.co.uk. Acesso em: 30 de maio 2007.
Nickerson D, Hunter P. (2006) The Noble cardiac ventricular electrophysiology models in CellML. Prog Biophys Mol Biol, Jan-Apr;90(1-3):346-59.
PCEnv (2008) Physiome CellML Environment. Disponível em: http://www.cellml.org/downloads/pcenv.
Pellet (2008) Pellet: The Open Source OWL DL Reasoner. Disponível em: http://pellet.owldl.com.
Protégé (2008) Protege OWL Ontology Editor for Semantic Web. Disponível em: http://protege.stanford.edu/plugins/owl/.
SPARQL. (2008) SPARQL Query Language for RDF. W3C Recommendation 15 January 2008. Disponível em: http://www.w3.org/TR/rdf-sparql-query/
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.
Bechhofer, S. et al. (2004) OWL web ontology language 1.0 reference. Disponível em: http://www.w3.org/TR/owl-ref/.
Bechhofer, S. et al (2005). The OWL Instance Store: System Description. Proceedings CADE-20, Lecture Notes in Computer Science, Springer-Verlag.
Borst, W.N. (1997) Construction of Engineering Ontologies. Phd Thesis. Disponível em: http://www.ub.utwente.nl/webdocs/inf/1/t0000004.pdf.
CellML (2008). Cell Markup Language. Disponível em http://www.cellml.org.
Garny A. et al. (2007) CellML and Associated Tools and Techniques. Paper submited to Elsevier Ireland Ltd.
GENSS (2005) GENSS Home Page, www. Disponível em http://genss.cs.bath.ac.uk/project.htm. Acesso em: 30 de maio 2007.
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.
Horrocks, I. et al. (2004) SWRL: A Semantic Web Rule Language Combining OWL and RuleML. W3C Member Submission 21 May 2004. http://www.w3.org/Submission/SWRL/.
Jess (2008) JESS, the Rule Engine for the Java Platform. Disponível em: http://herzberg.ca.sandia.gov.
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. (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: http://www.w3.org/Submission/OWL-S/.
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.
MONET (2006) MONET Consortium. MONET Home Page, www. Available from http://monet.nag.co.uk. Acesso em: 30 de maio 2007.
Nickerson D, Hunter P. (2006) The Noble cardiac ventricular electrophysiology models in CellML. Prog Biophys Mol Biol, Jan-Apr;90(1-3):346-59.
PCEnv (2008) Physiome CellML Environment. Disponível em: http://www.cellml.org/downloads/pcenv.
Pellet (2008) Pellet: The Open Source OWL DL Reasoner. Disponível em: http://pellet.owldl.com.
Protégé (2008) Protege OWL Ontology Editor for Semantic Web. Disponível em: http://protege.stanford.edu/plugins/owl/.
SPARQL. (2008) SPARQL Query Language for RDF. W3C Recommendation 15 January 2008. Disponível em: http://www.w3.org/TR/rdf-sparql-query/
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
20/08/2008
Como Citar
MATOS, Ely Edison; CAMPOS, Fernanda; BRAGA, Regina.
CelOWS: uma arquitetura orientada a serviços para definição, pesquisa e reuso de modelos biológicos. In: SIMPÓSIO BRASILEIRO DE COMPONENTES, ARQUITETURAS E REUTILIZAÇÃO DE SOFTWARE (SBCARS), 2. , 2008, Porto Alegre/RS.
Anais [...].
Porto Alegre: Sociedade Brasileira de Computação,
2008
.
p. 107-120.
DOI: https://doi.org/10.5753/sbcars.2008.46224.
