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Related Experiment Videos

Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation.

Magali Ruffier1, Andreas Kähäri1, Monika Komorowska1

  • 1European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Database : the Journal of Biological Databases and Curation
|April 3, 2017
PubMed
Summary

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Ensembl provides a robust software infrastructure for managing genome assemblies and functional annotations. This resource supports diverse species and integrates with other databases, facilitating genomic research and data sharing.

Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • The Ensembl software provides a stable infrastructure for storing, accessing, and manipulating genome assemblies and functional annotations.
  • Established over fifteen years ago, the Ensembl 'Core' database and Application Programming Interface (API) form the central component of Ensembl's genome resources.

Purpose of the Study:

  • To describe the Ensembl software resources and their evolution in managing the growing volume of genomic, transcriptomic, and proteomic data.
  • To highlight the expansion of the Ensembl framework to support a wider range of species and complex assembly models.
  • To emphasize the platform's utility for other research groups in generating and maintaining tailored genome annotations.

Main Methods:

  • Development and maintenance of a comprehensive software infrastructure for genome data management.

Related Experiment Videos

  • Integration of cross-referenced links to external informatics resources (e.g., UniProt, RefSeq) for enhanced data retrieval.
  • Public release of databases, APIs, and source code under a permissive license to encourage reuse and contributions.

    • Main Results:

    • The Ensembl framework has evolved to support numerous species beyond the human reference genome.
    • The system effectively integrates diverse genomic, transcriptomic, and proteomic datasets.
    • Cross-referencing with popular identifiers enhances searchability and data accessibility.
    • Ensembl serves as a valuable platform for custom genome annotation by external research groups.

    Conclusions:

    • Ensembl offers a comprehensive and robust solution for genome data management and annotation.
    • The platform's open accessibility and collaborative framework foster widespread adoption and contribution in genomic research.
    • Continued development ensures Ensembl remains a central resource for the global scientific community.