Extracting data with BioMart

Tables of Ensembl data can be downloaded via the highly customisable BioMart data mining tool. The easy-to-use web-based tool allows extraction of data without any programming knowledge or understanding of the underlying database structure.

BioMart tutorials and FAQs

• How to use BioMart
• BioMart tutorials: BioMart short videos and written materials.
• BioMart FAQs: BioMart Frequently Asked Questions.
  • How can I download all the proteins in the human proteome? Do I use BioMart?
  • Ensembl BioMart shows results for protein-coding genes when protein-associated attributes are chosen. Non-coding genes that pass filters will not be shown in the results if certain protein-associated attributes are chosen. Why does this occur?
• Combining multiple species datasets: Example on how to combine multiple mart datasets inside one mart or accross different marts.

BioMart R package, RESTful access and API

• BiomaRt, Bioconductor R package
• BioMart RESTful access (Perl and wget)
• BioMart perl API