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Related Experiment Videos

Accessing and distributing EMBL data using CORBA (common object request broker architecture).

L Wang1, P Rodriguez-Tomé, N Redaschi

  • 1EMBL Outstation - Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. lcwang@ebi.ac.uk

Genome Biology
|February 24, 2001
PubMed
Summary
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The EMBL Nucleotide Sequence Database now uses Common Object Request Broker Architecture (CORBA) for flexible data access, overcoming flat-file limitations. This enables researchers to build custom applications for efficient biological data querying and distribution.

Area of Science:

  • Bioinformatics
  • Molecular Biology Databases

Background:

  • The EMBL Nucleotide Sequence Database traditionally uses flat-file formats for DNA and RNA sequence data.
  • Flat files present limitations in flexibility and meeting diverse researcher needs for data querying and retrieval.
  • The Object Management Group's Common Object Request Broker Architecture (CORBA) offers a platform-independent standard for distributed object-oriented applications.

Purpose of the Study:

  • To develop a more flexible and efficient system for accessing and distributing data from the EMBL Nucleotide Sequence Database.
  • To leverage CORBA's capabilities for creating advanced biological data querying and distribution applications.

Main Methods:

  • Developed a CORBA infrastructure to provide an efficient interface for EMBL data.
  • Defined an EMBL object model for specifying interfaces in Interface Definition Language (IDL) to build CORBA servers.

Related Experiment Videos

  • Utilized PersistenceTM for mapping the object model to an Oracle relational database schema, implementing live object caching with an evictor pattern.

    • Main Results:

    • A CORBA infrastructure was successfully implemented, providing efficient access to and distribution of EMBL data.
    • The system allows for on-demand object creation and management through a live object cache.
    • The CORBA interfaces address the shortcomings of traditional flat-file formats.

    Conclusions:

    • CORBA interfaces offer an efficient solution for accessing and distributing EMBL database information.
    • Provides a flexible environment for researchers to develop custom client applications integrated with CORBA servers.
    • Enhances biological data management and accessibility for scientific research.