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An extensible application for assembling annotation for genomic data.

Jianhua Zhang1, Vincent Carey, Robert Gentleman

  • 1Department of Biostatistical Science, Dana-Farber Cancer Institute, Harvard School of Public Health, and Channing Laboratory, Boston, MA, USA. jzhang@jimmy.harvard.edu

Bioinformatics (Oxford, England)
|December 25, 2002
PubMed
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AnnBuilder is an R package that assembles genomic annotation data from multiple sources. It offers flexible data integration and outputs XML files for diverse system compatibility.

Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Genomic annotation data is crucial for biological research.
  • Existing systems may have limitations in data source flexibility.
  • Open-source tools facilitate wider adoption and development.

Purpose of the Study:

  • To introduce AnnBuilder, an R package for genomic annotation data assembly.
  • To provide a flexible system for integrating data from various sources.
  • To generate interoperable data formats for downstream applications.

Main Methods:

  • Development of an R package named AnnBuilder.
  • Implementation of parsers for LocusLink, Gene Ontology Consortium, and Human Gene Project data.
  • Design for extensibility with user-defined parsers for new data sources.

Related Experiment Videos

  • Output generation in XML format.

    • Main Results:

    • AnnBuilder successfully assembles genomic annotation data.
    • The package supports data integration from selected user sources.
    • Generated XML files are compatible with different systems.
    • The system is available as open-source via Bioconductor.

    Conclusions:

    • AnnBuilder provides a flexible and extensible solution for genomic annotation data assembly.
    • The package enhances data accessibility and usability through XML output.
    • It empowers researchers to create custom annotation datasets by integrating diverse sources.