At the core of CoGe is a relational database that stores any version of any genome from any organism in any state of assembly and annotation. This multi-genome database is a departure from many existing genome databases as it stores all these data in the same database. Overall, the schema for this database is rather simple, and this greatly aids in the database's ability to scale for many thousands of genomes while providing a database API that is straight-forward.
The database ids for each table are one of the primary ways that the web-tools of CoGe are linked together. Each table in the database has a unique id that can be used to directly get that set of information from the database. For example, each organism in CoGe has a unique database id, and these ids can be used to directly link to OrganismView to get information about a specific organism.