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How to use BioMart, Ensembl's data retrieval site


BioMart is the data access site of the Ensembl Genome Browser from EMBL-EBI. It contains data for the tracks in the Ensembl Genome Browser, and can be queried via the web or through R packages like biomaRt. This guide demonstrates the use of the BioMart web service.

Why use BioMart?

Sometimes you may want to retrieve sequences or genomic features in text (or table) format, without viewing them in a genome browser graphical view first. BioMart allows you to set your genome, filter by feature or region, and retrieve only the fields you want from the MANY tables of data available in Ensembl Genome Browser.

Examples of the use of BioMart:

  • Input a list of identifiers (gene symbols, Affymetrix IDs, NCBI protein, gene or nucleotide IDs, etc.) and use BioMart to retrieve the corresponding identifiers from a number of other molecular databases. It's an excellent conversion tool!
  • Retrieve all genes corresponding to a phenotype
  • Retrieve specific types of variants
  • Retrieve locations for a large list of regulatory features (more than can be obtained quickly in the browser)
  • Retrieve orthologous genes/sequences in another organism for your molecule(s) of interest
  • Many more potential uses

Accessing BioMart's Web Service

BioMart can be accessed from the Ensembl home page. When you go to the Ensembl home page, you may be directed to your nearest Ensembl web server/mirror (such as "US East" or "US West". If your nearest mirror is down for maintenance, you will be offered links to the other mirrors available.

Click on the "BioMart >" link in the Tools section at the top of the page, or the "BioMart" menu in the topmost menu of the site.

Screen shot of the Ensembl page with highlights on links to BioMart

You can also Google "Ensembl BioMart" and use links to access the web service.