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A cell-cycle knowledge integration framework

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Abstract
The goal of the EU FP6 project DIAMONDS 1 is to build a computational platform for studying the cell-cycle regulation process in several different (model) organisms (S. cerevisiae, S. pombe, A. thaliana and human). This platform will enable wet-lab biologists to use a systems biology approach encompassing data integration, modeling and simulation, thereby supporting analysis and interpretation of biochemical pathways involved in the cell cycle. To facilitate the computational handling of cell-cycle specific knowledge a detailed cell-cycle ontology is essential. The currently existing cell-cycle branch of the Gene Ontology (GO) provides only a static view and it is not rich enough to support in-depth cell-cycle studies. In this work, an enhanced Cell-Cycle Ontology (CCO) is proposed as an extension to existing GO. Besides the classical add-ons given by an ontology (data repository, knowledge sharing, validation, annotation, and so on), CCO is intended to further evolve into a knowledge-based system that provides reasoning services oriented to hypotheses evaluation in the context of cell-cycle studies. A data integration pipeline prototype, covering the entire life cycle of the knowledge base, is presented. Concrete problems and initial results related to the implementation of automatic format mappings between ontologies and inconsistency checking issues are discussed in detail.
Keywords
INFORMATICS, DATABASE, GENE ONTOLOGY GO, CANCER

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Please use this url to cite or link to this publication:

Chicago
Antezana San Roman, Erick Zimar, Elena Tsiporkova, Vladimir Mironov, and Martin Kuiper. 2006. “A Cell-cycle Knowledge Integration Framework.” Ed. U Leser, F Neumann, and B Eckman. Lecture Notes in Computer Science 4075: 19–34.
APA
Antezana San Roman, E. Z., Tsiporkova, E., Mironov, V., & Kuiper, M. (2006). A cell-cycle knowledge integration framework. (U. Leser, F. Neumann, & B. Eckman, Eds.)Lecture Notes in Computer Science, 4075, 19–34. Presented at the 3rd International workshop on Data Integration in the Life Sciences (DILS 2006).
Vancouver
1.
Antezana San Roman EZ, Tsiporkova E, Mironov V, Kuiper M. A cell-cycle knowledge integration framework. Leser U, Neumann F, Eckman B, editors. Lecture Notes in Computer Science. Berlin, Germany: Springer; 2006;4075:19–34.
MLA
Antezana San Roman, Erick Zimar, Elena Tsiporkova, Vladimir Mironov, et al. “A Cell-cycle Knowledge Integration Framework.” Ed. U Leser, F Neumann, & B Eckman. Lecture Notes in Computer Science 4075 (2006): 19–34. Print.
@article{372272,
  abstract     = {The goal of the EU FP6 project DIAMONDS 1 is to build a computational platform for studying the cell-cycle regulation process in several different (model) organisms (S. cerevisiae, S. pombe, A. thaliana and human). This platform will enable wet-lab biologists to use a systems biology approach encompassing data integration, modeling and simulation, thereby supporting analysis and interpretation of biochemical pathways involved in the cell cycle. To facilitate the computational handling of cell-cycle specific knowledge a detailed cell-cycle ontology is essential. The currently existing cell-cycle branch of the Gene Ontology (GO) provides only a static view and it is not rich enough to support in-depth cell-cycle studies. 
In this work, an enhanced Cell-Cycle Ontology (CCO) is proposed as an extension to existing GO. Besides the classical add-ons given by an ontology (data repository, knowledge sharing, validation, annotation, and so on), CCO is intended to further evolve into a knowledge-based system that provides reasoning services oriented to hypotheses evaluation in the context of cell-cycle studies. A data integration pipeline prototype, covering the entire life cycle of the knowledge base, is presented. Concrete problems and initial results related to the implementation of automatic format mappings between ontologies and inconsistency checking issues are discussed in detail.},
  author       = {Antezana San Roman, Erick Zimar and Tsiporkova, Elena and Mironov, Vladimir and Kuiper, Martin},
  editor       = {Leser, U and Neumann, F and Eckman, B},
  isbn         = {9783540365952},
  issn         = {0302-9743},
  journal      = {Lecture Notes in Computer Science},
  language     = {eng},
  location     = {Hinxton, UK},
  pages        = {19--34},
  publisher    = {Springer},
  title        = {A cell-cycle knowledge integration framework},
  url          = {http://dx.doi.org/10.1007/11799511\_4},
  volume       = {4075},
  year         = {2006},
}

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