Ensembl uses MySQL relational databases to store its information. A comprehensive set of Application Programme Interfaces (APIs) serve as a middle-layer between underlying database schemes and more specific application programmes. The APIs aim to encapsulate the database layout by providing efficient high-level access to data tables and isolate applications from data layout changes. Ensembl provides an API in Perl.
The set of species-specific Ensembl Core databases stores genome sequences and most of the annotation information. This includes the gene, transcript and protein models annotated by the Ensembl automated genome analysis and annotation pipeline. Ensembl Core databases also store assembly information, cDNA and protein alignments, external references, markers and repeat regions data sets.
Species-specific Ensembl OtherFeatures databases hold an independent EST gene set provided for all well-characterised species with a suitable amount of biological evidence. The layout of Ensembl OtherFeatures Databases is identical to the Ensembl Core Database schema so that schema descriptions and API access are equally applicable.
The Ensembl Compara multi-species database stores the results of genome-wide species comparisons re-calculated for each release. The comparative genomics set includes pairwise whole genome alignments and synteny regions. The comparative proteomics data set contains orthologue predictions and protein family clusters.
The large amount of genetic variation information is organised in a set of species-specific Ensembl Variation databases.
The funcgen databases store genome wide functional genomics and regulatory information. These data are used to produce the Ensembl 'Regulatory Build'.
The Registry system allows to tell your programs where to find the EnsEMBL databases and how to connect to them. It has been implemented for the Ensembl Core and Compara APIs.
Ensembl is an open project and we would like to encourage correspondence and discussions on any subject on any aspect of Ensembl. Please see the Ensembl Contacts page for suitable options for getting in touch with us.