Orymold : ontology based gene expression data integration and analysis tool applied to rice
Mercadé, Jaume (Parc Científic de Barcelona. Oryzon Genomics)
Espinosa, Antonio (Parc Científic de Barcelona. Oryzon Genomics)
Adsuara, José-Enrique (Parc Científic de Barcelona. Oryzon Genomics)
Adrados, Rosa (Parc Científic de Barcelona. Oryzon Genomics)
Segura, Jordi (Parc Científic de Barcelona. Oryzon Genomics)
Puigdomènech, Pere, 1948- (Parc Científic de Barcelona. Oryzon Genomics)
Maes, Tamara (Parc Científic de Barcelona. Oryzon Genomics)

Date:	2009
Abstract:	Background: Integration and exploration of data obtained from genome wide monitoring technologies has become a major challenge for many bioinformaticists and biologists due to its heterogeneity and high dimensionality. A widely accepted approach to solve these issues has been the creation and use of controlled vocabularies (ontologies). Ontologies allow for the formalization of domain knowledge, which in turn enables generalization in the creation of querying interfaces as well as in the integration of heterogeneous data, providing both human and machine readable interfaces. Results: We designed and implemented a software tool that allows investigators to create their own semantic model of an organism and to use it to dynamically integrate expression data obtained from DNA microarrays and other probe based technologies. The software provides tools to use the semantic model to postulate and validate of hypotheses on the spatial and temporal expression and function of genes. In order to illustrate the software's use and features, we used it to build a semantic model of rice (Oryza sativa) and integrated experimental data into it. Conclusion: In this paper we describe the development and features of a flexible software application for dynamic gene expression data annotation, integration, and exploration called Orymold. Orymold is freely available for non-commercial users from http://www. oryzon. com/media/orymold. html webcite.
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; Versió publicada
Published in:	BMC bioinformatics, Vol. 10, N. 158 (May 2009) , p. 1-12, ISSN 1471-2105

DOI: 10.1186/1471-2105-10-158
PMID: 19463186

12 p, 611.8 KB

Additional file 1 2 p, 83.7 KB

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