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Review
. 2004 May;14(5):929-33.
doi: 10.1101/gr.1857204.

The Ensembl core software libraries

Arne Stabenau  1 , Graham McVicker, Craig Melsopp, Glenn Proctor, Michele Clamp, Ewan Birney
Affiliations
Review

The Ensembl core software libraries

Arne Stabenau et al. Genome Res. 2004 May.

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.

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Figures

Figure 1
Figure 1
Entity relationship model of the Ensembl schema. Tables are represented as divided rectangles consisting of a boldface table name at the top and a list of table attributes and attribute types below. Internal identifiers and join tables are omitted. Relationships between tables are represented by lines labeled with the relationship type: 1___1...n one to one-or-many relationship; 1___1 one-to-one relationship; 1___0...n one to zero-or-many relationship; 1...n___1...n one-or-many to one-or-many relationship; 1...2___0...n one-or-two to zero-or-many relationship.
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WEB SITE REFERENCES

    1. http://www.ensembl.org/Docs/ensembl_tutorial.pdf; Ensembl online tutorial document.

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