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R. Ripp, G. Berthommier, L. Poidevin, H. N. Nguyen, T. Léveillard, O. Lorentz, E. Zrenner, J. A. Sahel, O. Poch; The Evi-Genoret Database: Collecting, Managing and Publishing Heterogeneous Clinical and Biological Data to Create and Federate Knowledge About Retinal Diseases. Invest. Ophthalmol. Vis. Sci. 2008;49(13):5209. doi: https://doi.org/.
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EVI-Genoret Database, developed as part of the European Integrated Project EVI-GENORET "functional genomics of the retina in development, health and disease", provides an infrastructure for managing and systematising biological sample handling and processing, data acquisition and analysis, and templates for data storage, data mining and integration
It is a SQL relational database based on the Object Relational Mapping paradigm. High throughput data (transcriptomics, proteomics, ...) processing is done by the Bioconductor package. Unifying hierarchical integration and connection of the bioinformatics, functional genomics, patient, phenotyping and clinical data are performed by the in-house EVI-Gscope platform. Knowledge extraction is performed through the DB2 Intelligent Miner. Publishing of the data is done through standard and dynamic web technologies (PHP, HTML).
As a collaborative platform for the retinal community, the EVI-Genoret Database federates tools (common or custom) and resources (local and external databases) around three main axes of data organisation and processing, namely Patients, Genes and Standards. It already integrates a large amount of heterogeneous data concerning patient records (6000), annotated eye-fundus and in situ hybridisation images (1751), retinal gene analyses and networks (3699), functional genomics experiments (308), standardized operating protocols and experiments (65). The automated network system processes local and distant data allowing standardized and complex analysis, correlation studies and knowledge discovery. To ensure efficient exploitation of the database by users, an ergonomic and attractive design and an intuitive navigation system have been developed for querying and visualization.
The developed data network allows effective exploitation and access to interconnected and unified heterogeneous retinal information linking mutation, polymorphism, pathologies and clinical data, tissue and cellular expression as well as animal models. Thus, the EVI-Genoret Database philosophy represents a novel prototypic information network, immersing heterogeneous data in the integration and correlation processes, paving the way for computer-aided diagnosis, disease screening, drug target evaluation and the development of new therapeutics.
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