Download data with BioMart

Much of Ensembl's data can be quickly exported in text format, as an Excel table, or as FASTA sequences through the BioMart interface.

 BioMart allows you to:

  • ‘Translate’ one ID type into another (for example, an Ensembl gene ID to an NCBI RefSeqID;
  • Export data in different formats, including: html, csv, tsv and xls (Excel) file types;
  • Quickly generate tables of information.
Figure 44. Access BioMart from the top of Ensembl pages to export genes, variations and sequences.

You can use the 'Biomart' link at the top of every Ensembl page to access BioMart (Figure 44).

Database. You can choose the database you are interested in. In our example, we have selected the Ensembl genes database, version 89.

Dataset. You can choose the dataset you want to access. In our example we chose the Human data set.

Options. Apply filters on the data set in order to select a set of genes of interest. Attributes allow you to select output options.  Addtional datasets can be combined in your query as an advanced function.


This tutorial is a good guide for getting started.

You can also view the Ensembl FAQs page.