Download data with BioMart

Downloading 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 is a quick data mining tool, or data management system supported by the Ontario Institute for Cancer Research (OICR) and the EBI.

 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.

Accessing BioMart from the Ensembl pages
Figure 41. Access BioMart from the top of Ensembl pages to export genes, variations and sequences.

You can visit the central portal to BioMart.

NotesBioMart link. You can use the 'Biomart' link at the top of every Ensembl page to access BioMart (circled in Figure 41, above).

Database. You can choose the database [A] you are interested in. In our example, we have selected the Ensembl genes database, version 63.

Dataset. You can choose the dataset [B] you want to access. In our example we chose the Homo sapiens 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 [C].


This tutorial is a good guide for getting started.

You can also view the Ensembl FAQs page.