Alternative Access Methods
In addition to its website, Ensembl provides a Perl API (Application Programming Interface) that models biological objects such as genes and proteins, allowing simple scripts to be written to retrieve data of interest. The same API is used internally by the web interface to display the data. It is divided in sections like the core API, the compara API (for comparative genomics data), the variation API (for accessing SNPs, SNVs, CNVs..), and the functional genomics API (to access regulatory data). The Ensembl website provides extensive information on how to install and use the API.
This software can be used to access the public MySQL database, avoiding the need to download enormous datasets. The users could even choose to retrieve data from the MySQL with direct SQL queries, but this requires an extensive knowledge of the current database schema.
Large datasets can be retrieved using the BioMart data-mining tool. It provides a web interface for downloading datasets using complex queries.
Last, there is an FTP server which can be used to download entire MySQL databases as well some selected data sets in other formats.
Read more about this topic: Ensembl
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