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Related Experiment Videos

XEMBL: distributing EMBL data in XML format.

Lichun Wang1, Jean-Jack Riethoven, Alan Robinson

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

Bioinformatics (Oxford, England)
|August 15, 2002
PubMed
Summary
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The EMBL Nucleotide Sequence Database now offers data in XML format via the XEMBL service, overcoming flat-file limitations for better data exchange and accessibility.

Area of Science:

  • Bioinformatics
  • Genomic Databases

Background:

  • Traditional EMBL Nucleotide Sequence Database data distribution uses flat files with inherent limitations.
  • Extensible Markup Language (XML) is emerging as a standard for data exchange, offering structured syntax and defined data formats.
  • There is a growing demand for EMBL data to be available in an XML format.

Purpose of the Study:

  • To address the shortcomings of flat-file data distribution from the EMBL Nucleotide Sequence Database.
  • To provide EMBL data in a more structured and accessible XML format.
  • To develop a service tool for efficient distribution of EMBL data in XML.

Main Methods:

  • The XEMBL service tool was developed to access EMBL data.
  • CORBA (Common Object Request Broker Architecture) servers are employed to retrieve data.

Related Experiment Videos

  • Data is distributed in XML format through various mechanisms.

    • Main Results:

    • The XEMBL service provides EMBL data in XML format.
    • This overcomes the limitations associated with traditional flat-file formats.
    • Data is accessible via web forms, CGI, and a SOAP-enabled service.

    Conclusions:

    • The XEMBL service successfully distributes EMBL Nucleotide Sequence Database data in XML format.
    • This facilitates improved data exchange and utilization in bioinformatics.
    • The service is freely available and accessible through multiple interfaces.