May 2008
Volume 49, Issue 13
Free
ARVO Annual Meeting Abstract  |   May 2008
The Evi-Genoret Database: Collecting, Managing and Publishing Heterogeneous Clinical and Biological Data to Create and Federate Knowledge About Retinal Diseases
Author Affiliations & Notes
  • R. Ripp
    IGBMC, Strasbourg Illkirch, France
  • G. Berthommier
    IGBMC, Strasbourg Illkirch, France
  • L. Poidevin
    IGBMC, Strasbourg Illkirch, France
  • H. N. Nguyen
    IGBMC, Strasbourg Illkirch, France
  • T. Léveillard
    Laboratoire de Physiopathologie Cellulaire et Moléculaire de la Rétine, Paris, France
  • O. Lorentz
    Laboratoire de Physiopathologie Cellulaire et Moléculaire de la Rétine, Paris, France
  • E. Zrenner
    University Eye Hospital, Tuebingen, Germany
  • J. A. Sahel
    Laboratoire de Physiopathologie Cellulaire et Moléculaire de la Rétine, Paris, France
  • O. Poch
    IGBMC, Strasbourg Illkirch, France
  • Footnotes
    Commercial Relationships  R. Ripp, None; G. Berthommier, None; L. Poidevin, None; H.N. Nguyen, None; T. Léveillard, None; O. Lorentz, None; E. Zrenner, None; J.A. Sahel, None; O. Poch, None.
  • Footnotes
    Support  EVI-GENORET FP6 Integrated Project LSHG-CT-2005-512036, RETNET MRTN-CN-2003-504003, the Decrypthon program initiated by Association Française contre les Myopathies, ULP, CNRS, INSERM
Investigative Ophthalmology & Visual Science May 2008, Vol.49, 5209. doi:
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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.

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      © ARVO (1962-2015); The Authors (2016-present)

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Abstract

Purpose: : 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

Methods: : 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).

Results: : 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.

Conclusions: : 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.

Keywords: retina • computational modeling • candidate gene analysis 
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