title: Orymold: ontology based gene expression data integration and analysis tool applied to rice.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Oryzon Genomics, Parc Científic de Barcelona, 08028 Barcelona, Spain. jmercade@oryzon.com
authors.forename: Jaume
authors.initials: J
authors.lastname: Mercadé
authors.forename: Antonio
authors.initials: A
authors.lastname: Espinosa
authors.forename: José-Enrique
authors.initials: JE
authors.lastname: Adsuara
authors.forename: Rosa
authors.initials: R
authors.lastname: Adrados
authors.forename: Jordi
authors.initials: J
authors.lastname: Segura
authors.forename: Tamara
authors.initials: T
authors.lastname: Maes
mesh_terms: D030541:Databases, Genetic; D015870:Gene Expression; D023281:Genomics / Q000379:methods*; D007091:Image Processing, Computer-Assisted / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012275:Oryza / Q000235:genetics*; D015203:Reproducibility of Results; D012660:Semantics; D012984:Software; D014584:User-Computer Interface; D018875:Vocabulary, Controlled