The Ensembl Core Software Libraries

  1. Arne Stabenau1,
  2. Graham McVicker1,
  3. Craig Melsopp1,
  4. Glenn Proctor1,
  5. Michele Clamp2, and
  6. Ewan Birney1,3
  1. 1 EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
  2. 2 The Broad Institute, Cambridge, Massachusetts 02141-2023, USA

Abstract

Systems for managing genomic data must store a vast quantity of information. Ensembl stores these data in several MySQL databases. The core software libraries provide a practical and effective means for programmers to access these data. By encapsulating the underlying database structure, the libraries present end users with a simple, abstract interface to a complex data model. Programs that use the libraries rather than SQL to access the data are unaffected by most schema changes. The architecture of the core software libraries, the schema, and the factors influencing their design are described. All code and data are freely available.

Footnotes

  • Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.1857204.

  • ↵3 Corresponding author. E-MAIL birney{at}ebi.ac.uk; FAX 44-1223-494468.

    • Accepted February 25, 2004.
    • Received August 8, 2003.
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  1. doi: 10.1101/gr.1857204 Genome Res. 14: 929-933 Cold Spring Harbor Laboratory Press

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