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The otter annotation system.

Stephen M J Searle1, James Gilbert, Vivek Iyer

  • 1The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

Genome Research
|May 5, 2004
PubMed
Summary
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The Otter manual annotation system extends Ensembl to manage large-scale genome annotation data. This system supports manual curation and improvement of genome sequences for future research.

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • The completion of the human genome sequence necessitates efficient manual annotation.
  • Existing tools like Ensembl lack support for essential manual annotation textual data.
  • Accurate and improvable genome annotation is crucial for future biological research.

Purpose of the Study:

  • To develop a robust system for manual genome annotation.
  • To extend Ensembl's capabilities for managing complex annotation data.
  • To facilitate collaborative and scalable genome annotation efforts.

Main Methods:

  • Developed the Otter manual annotation system, including a relational database schema.
  • Created an application-programming interface (API) for data access.

Related Experiment Videos

  • Implemented an extensible markup language (XML) format for data transfer and a server for multi-user access.
  • Developed a data-adaptor plugin for the Apollo Browser/Editor.

    • Main Results:

    • The Otter system provides a comprehensive solution for storing and accessing manual annotation data.
    • The system is integrated with the Vertebrate Genome Annotation (VEGA) site for human chromosome annotation.
    • Support is underway for the AceDB annotation editor (FMap) via Lace.

    Conclusions:

    • The Otter system effectively addresses the need for advanced manual genome annotation tools.
    • It enhances the capability to curate and improve genome annotations, supporting ongoing research.
    • The system is actively used by the Human and Vertebrate Annotation (HAVANA) group for human chromosome annotation.