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
Famous quotes containing the words alternative, access and/or methods:
“If you have abandoned one faith, do not abandon all faith. There is always an alternative to the faith we lose. Or is it the same faith under another mask?”
—Graham Greene (1904–1991)
“The nature of women’s oppression is unique: women are oppressed as women, regardless of class or race; some women have access to significant wealth, but that wealth does not signify power; women are to be found everywhere, but own or control no appreciable territory; women live with those who oppress them, sleep with them, have their children—we are tangled, hopelessly it seems, in the gut of the machinery and way of life which is ruinous to us.”
—Andrea Dworkin (b. 1946)
“The methods by which a trade union can alone act, are necessarily destructive; its organization is necessarily tyrannical.”
—Henry George (1839–1897)