Ensembl is a joint project between EMBL-EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on eukaryotic genomes.
Ensembl's relational schema is available on-line. Go to the Ensembl development web page, and follow link to "Ensembl WebCVS Repository". From there, follow "ensembl/" then "sql/" then "table.sql". You will see from the revision numbers and dates that the schema is still evolving. To see the table creation statements for any particular revision click on the revision number.
ArrayExpress is a public repository for microarray based gene expression data.
ArrayExpress' relational schema is available on-line. Go to the ArrayExpress Implementation then click on MAGE-RS.sql to see the table creation statements.
A relational schema is being designed for SWISS-PROT in a project at the European Bioinformatics Institute. Look at some of the schema diagrams.
Look at the ensemblFDM and aeFDM schemas and web interfaces. See how Daplex queries against the ensemblFDM schema are translated to SQL.