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Orymold: ontology based gene expression data integration and analysis tool applied to rice.

Mercadé J, Espinosa A, Adsuara JE, Adrados R, Segura J, Maes T - BMC Bioinformatics (2009)

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Oryzon Genomics, Parc Científic de Barcelona, 08028 Barcelona, Spain. jmercade@oryzon.com

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.

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Unified Modelling Language (UML 2.0) deployment diagram of Orymold system. Orymold is a distributed system composed of a client and an annotations database server. The annotations server, OryDB, stores annotations from TIGR using its publicly available FTP server through the OryDBdata component. The OryDBcon component from OryDB provides a web service for retrieving annotations and mapping sequences as requested by the Orymold remote client. The Orymold client component communicates with the OryDB system through its RMI interface, and manages data stored in the experimental database. It has to be noted that the experimental database could be distributed and serve as a common experimental data warehouse for several clients.
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Figure 2: Unified Modelling Language (UML 2.0) deployment diagram of Orymold system. Orymold is a distributed system composed of a client and an annotations database server. The annotations server, OryDB, stores annotations from TIGR using its publicly available FTP server through the OryDBdata component. The OryDBcon component from OryDB provides a web service for retrieving annotations and mapping sequences as requested by the Orymold remote client. The Orymold client component communicates with the OryDB system through its RMI interface, and manages data stored in the experimental database. It has to be noted that the experimental database could be distributed and serve as a common experimental data warehouse for several clients.

Mentions: OryDB is organized in two layers: a persistence layer and a management and connection layer. The persistence layer is implemented using a RDBMS that allows for relational organization of the information and easy customisation of indexes for fast query, retrieval, and parsing of the results. We developed a Java code layer to manage and process data, populate and update the database, perform remote BLAST [12], and provide fast connection and extension with the Orymold client through web services implemented using the Java Remote Method Invocation (RMI) API (see Fig. 2). Thus, OryDB can be considered an autonomous system providing annotations through its web services interface.


Orymold: ontology based gene expression data integration and analysis tool applied to rice.

Mercadé J, Espinosa A, Adsuara JE, Adrados R, Segura J, Maes T - BMC Bioinformatics (2009)

Unified Modelling Language (UML 2.0) deployment diagram of Orymold system. Orymold is a distributed system composed of a client and an annotations database server. The annotations server, OryDB, stores annotations from TIGR using its publicly available FTP server through the OryDBdata component. The OryDBcon component from OryDB provides a web service for retrieving annotations and mapping sequences as requested by the Orymold remote client. The Orymold client component communicates with the OryDB system through its RMI interface, and manages data stored in the experimental database. It has to be noted that the experimental database could be distributed and serve as a common experimental data warehouse for several clients.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2696451&req=5

Figure 2: Unified Modelling Language (UML 2.0) deployment diagram of Orymold system. Orymold is a distributed system composed of a client and an annotations database server. The annotations server, OryDB, stores annotations from TIGR using its publicly available FTP server through the OryDBdata component. The OryDBcon component from OryDB provides a web service for retrieving annotations and mapping sequences as requested by the Orymold remote client. The Orymold client component communicates with the OryDB system through its RMI interface, and manages data stored in the experimental database. It has to be noted that the experimental database could be distributed and serve as a common experimental data warehouse for several clients.
Mentions: OryDB is organized in two layers: a persistence layer and a management and connection layer. The persistence layer is implemented using a RDBMS that allows for relational organization of the information and easy customisation of indexes for fast query, retrieval, and parsing of the results. We developed a Java code layer to manage and process data, populate and update the database, perform remote BLAST [12], and provide fast connection and extension with the Orymold client through web services implemented using the Java Remote Method Invocation (RMI) API (see Fig. 2). Thus, OryDB can be considered an autonomous system providing annotations through its web services interface.

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Oryzon Genomics, Parc Científic de Barcelona, 08028 Barcelona, Spain. jmercade@oryzon.com

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.

Show MeSH